2GLJ | pdb_00002glj

crystal structure of aminopeptidase I from Clostridium acetobutylicum

PDB DOI: https://doi.org/10.2210/pdb2GLJ/pdb

Classification: HYDROLASE
Organism(s): Clostridium acetobutylicum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-04-04 Released: 2006-06-13
Deposition Author(s): Min, T., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.297 (Depositor), 0.290 (DCC)
R-Value Work:
0.250 (Depositor), 0.250 (DCC)
R-Value Observed:
0.250 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

crystal structure of aminopeptidase I from Clostridium acetobutylicum

Min, T., Shapiro, L.

To be published.

Macromolecule Content

Total Structure Weight: 1,242.59 kDa
Atom Count: 91,225
Modelled Residue Count: 10,944
Deposited Residue Count: 11,064
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable M18-family aminopeptidase 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	461	Clostridium acetobutylicum	Mutation(s): 1 Gene Names: apeA EC: 3.4.11
UniProt
Find proteins for Q97K30 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97K30 Go to UniProtKB: Q97K30
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q97K30
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain GB [auth R] SDF format, chain LA [auth G] SDF format, chain WA [auth M] SDF format, chain AA [auth B] SDF format, chain AB [auth O] SDF format, chain BA [auth B] SDF format, chain BB [auth O] SDF format, chain CA [auth C] SDF format, chain CB [auth P] SDF format, chain DA [auth C] SDF format, chain DB [auth P] SDF format, chain EA [auth D] SDF format, chain EB [auth Q] SDF format, chain FA [auth D] SDF format, chain FB [auth Q] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain HB [auth R] SDF format, chain IA [auth F] SDF format, chain IB [auth S] SDF format, chain JA [auth F] SDF format, chain JB [auth S] SDF format, chain KA [auth G] SDF format, chain KB [auth T] SDF format, chain LB [auth T] SDF format, chain MA [auth H] SDF format, chain MB [auth U] SDF format, chain NA [auth H] SDF format, chain NB [auth U] SDF format, chain OA [auth I] SDF format, chain OB [auth V] SDF format, chain PA [auth I] SDF format, chain PB [auth V] SDF format, chain QA [auth J] SDF format, chain QB [auth W] SDF format, chain RA [auth J] SDF format, chain RB [auth W] SDF format, chain SA [auth K] SDF format, chain SB [auth X] SDF format, chain TA [auth K] SDF format, chain TB [auth X] SDF format, chain UA [auth L] SDF format, chain VA [auth L] SDF format, chain XA [auth M] SDF format, chain Y [auth A] SDF format, chain YA [auth N] SDF format, chain Z [auth A] SDF format, chain ZA [auth N] MOL2 format, chain GB [auth R] MOL2 format, chain LA [auth G] MOL2 format, chain WA [auth M] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth O] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth O] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth P] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth P] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth Q] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth Q] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain HB [auth R] MOL2 format, chain IA [auth F] MOL2 format, chain IB [auth S] MOL2 format, chain JA [auth F] MOL2 format, chain JB [auth S] MOL2 format, chain KA [auth G] MOL2 format, chain KB [auth T] MOL2 format, chain LB [auth T] MOL2 format, chain MA [auth H] MOL2 format, chain MB [auth U] MOL2 format, chain NA [auth H] MOL2 format, chain NB [auth U] MOL2 format, chain OA [auth I] MOL2 format, chain OB [auth V] MOL2 format, chain PA [auth I] MOL2 format, chain PB [auth V] MOL2 format, chain QA [auth J] MOL2 format, chain QB [auth W] MOL2 format, chain RA [auth J] MOL2 format, chain RB [auth W] MOL2 format, chain SA [auth K] MOL2 format, chain SB [auth X] MOL2 format, chain TA [auth K] MOL2 format, chain TB [auth X] MOL2 format, chain UA [auth L] MOL2 format, chain VA [auth L] MOL2 format, chain XA [auth M] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth N] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth N] mmCIF format, chain GB [auth R] mmCIF format, chain LA [auth G] mmCIF format, chain WA [auth M] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth O] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth O] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth P] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth P] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth Q] mmCIF format, chain FA [auth D] mmCIF format, chain FB [auth Q] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain HB [auth R] mmCIF format, chain IA [auth F] mmCIF format, chain IB [auth S] mmCIF format, chain JA [auth F] mmCIF format, chain JB [auth S] mmCIF format, chain KA [auth G] mmCIF format, chain KB [auth T] mmCIF format, chain LB [auth T] mmCIF format, chain MA [auth H] mmCIF format, chain MB [auth U] mmCIF format, chain NA [auth H] mmCIF format, chain NB [auth U] mmCIF format, chain OA [auth I] mmCIF format, chain OB [auth V] mmCIF format, chain PA [auth I] mmCIF format, chain PB [auth V] mmCIF format, chain QA [auth J] mmCIF format, chain QB [auth W] mmCIF format, chain RA [auth J] mmCIF format, chain RB [auth W] mmCIF format, chain SA [auth K] mmCIF format, chain SB [auth X] mmCIF format, chain TA [auth K] mmCIF format, chain TB [auth X] mmCIF format, chain UA [auth L] mmCIF format, chain VA [auth L] mmCIF format, chain XA [auth M] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth N] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth N]	AA [auth B] AB [auth O] BA [auth B] BB [auth O] CA [auth C] AA [auth B], AB [auth O], BA [auth B], BB [auth O], CA [auth C], CB [auth P], DA [auth C], DB [auth P], EA [auth D], EB [auth Q], FA [auth D], FB [auth Q], GA [auth E], GB [auth R], HA [auth E], HB [auth R], IA [auth F], IB [auth S], JA [auth F], JB [auth S], KA [auth G], KB [auth T], LA [auth G], LB [auth T], MA [auth H], MB [auth U], NA [auth H], NB [auth U], OA [auth I], OB [auth V], PA [auth I], PB [auth V], QA [auth J], QB [auth W], RA [auth J], RB [auth W], SA [auth K], SB [auth X], TA [auth K], TB [auth X], UA [auth L], VA [auth L], WA [auth M], XA [auth M], Y [auth A], YA [auth N], Z [auth A], ZA [auth N]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth O] Focus chain BA [auth B] Focus chain BB [auth O] Focus chain CA [auth C] Focus chain CB [auth P] Focus chain DA [auth C] Focus chain DB [auth P] Focus chain EA [auth D] Focus chain EB [auth Q] Focus chain FA [auth D] Focus chain FB [auth Q] Focus chain GA [auth E] Focus chain GB [auth R] Focus chain HA [auth E] Focus chain HB [auth R] Focus chain IA [auth F] Focus chain IB [auth S] Focus chain JA [auth F] Focus chain JB [auth S] Focus chain KA [auth G] Focus chain KB [auth T] Focus chain LA [auth G] Focus chain LB [auth T] Focus chain MA [auth H] Focus chain MB [auth U] Focus chain NA [auth H] Focus chain NB [auth U] Focus chain OA [auth I] Focus chain OB [auth V] Focus chain PA [auth I] Focus chain PB [auth V] Focus chain QA [auth J] Focus chain QB [auth W] Focus chain RA [auth J] Focus chain RB [auth W] Focus chain SA [auth K] Focus chain SB [auth X] Focus chain TA [auth K] Focus chain TB [auth X] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain WA [auth M] Focus chain XA [auth M] Focus chain Y [auth A] Focus chain YA [auth N] Focus chain Z [auth A] Focus chain ZA [auth N] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth O] Focus chain BA [auth B] Focus chain BB [auth O] Focus chain CA [auth C] Focus chain CB [auth P] Focus chain DA [auth C] Focus chain DB [auth P] Focus chain EA [auth D] Focus chain EB [auth Q] Focus chain FA [auth D] Focus chain FB [auth Q] Focus chain GA [auth E] Focus chain GB [auth R] Focus chain HA [auth E] Focus chain HB [auth R] Focus chain IA [auth F] Focus chain IB [auth S] Focus chain JA [auth F] Focus chain JB [auth S] Focus chain KA [auth G] Focus chain KB [auth T] Focus chain LA [auth G] Focus chain LB [auth T] Focus chain MA [auth H] Focus chain MB [auth U] Focus chain NA [auth H] Focus chain NB [auth U] Focus chain OA [auth I] Focus chain OB [auth V] Focus chain PA [auth I] Focus chain PB [auth V] Focus chain QA [auth J] Focus chain QB [auth W] Focus chain RA [auth J] Focus chain RB [auth W] Focus chain SA [auth K] Focus chain SB [auth X] Focus chain TA [auth K] Focus chain TB [auth X] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain WA [auth M] Focus chain XA [auth M] Focus chain Y [auth A] Focus chain YA [auth N] Focus chain Z [auth A] Focus chain ZA [auth N]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.297 (Depositor), 0.290 (DCC)
R-Value Work: 0.250 (Depositor), 0.250 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.708	α = 89.88
b = 129.68	β = 90
c = 222.728	γ = 116.68

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-06-13

Deposition Author(s):

Min, T.

Shapiro, L.

Burley, S.K.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2006-06-13
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-11-13
Changes: Data collection, Database references, Structure summary