5W79 | pdb_00005w79

Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis, Cysteine-less mutant in the Apo State

PDB DOI: https://doi.org/10.2210/pdb5W79/pdb

Classification: CHAPERONE
Organism(s): Methanococcus maripaludis
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2017-06-19 Released: 2018-06-20
Deposition Author(s): Dalton, K.M., Lopez, T., Liu, C., Ralston, C.Y., Pereira, J.H., Chartron, J.W., McAndrew, R.P., Douglas, N.R., Adams, P.D., Pande, V.S., Frydman, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.12 Å
R-Value Free:
0.281 (Depositor), 0.282 (DCC)
R-Value Work:
0.249 (Depositor), 0.250 (DCC)
R-Value Observed:
0.251 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The Conformational Cycle of the Group II Chaperonin Termini

Dalton, K.M., Lopez, T., Liu, C., Ralston, C.Y., Pereira, J.H., Chartron, J.W., McAndrew, R.P., Douglas, N.R., Adams, P.D., Pande, V.S., Frydman, J.

To be published.

Macromolecule Content

Total Structure Weight: 468.05 kDa
Atom Count: 31,143
Modeled Residue Count: 4,120
Deposited Residue Count: 4,344
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin	A, B, C, D, E A, B, C, D, E, F, G, H	543	Methanococcus maripaludis	Mutation(s): 8
UniProt
Find proteins for Q6LX38 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL)) Explore Q6LX38 Go to UniProtKB: Q6LX38
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6LX38
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.12 Å
R-Value Free: 0.281 (Depositor), 0.282 (DCC)
R-Value Work: 0.249 (Depositor), 0.250 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.98	α = 90
b = 149.98	β = 90
c = 416.477	γ = 120

Software Package:

Software Name	Purpose
iMOSFLM	data processing
SCALA	data reduction
PHASER	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-06-20
Type: Initial release
Version 1.1: 2018-08-29
Changes: Data collection, Database references
Version 1.2: 2024-12-25
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary

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Deposit Data

Help and Resources

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Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis, Cysteine-less mutant in the Apo State

The Conformational Cycle of the Group II Chaperonin Termini

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

5W79 | pdb_00005w79