1T3H | pdb_00001t3h

X-ray Structure of Dephospho-CoA Kinase from E. coli Norteast Structural Genomics Consortium Target ER57

PDB DOI: https://doi.org/10.2210/pdb1T3H/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-04-26 Released: 2004-05-11
Deposition Author(s): Kuzin, A.P., Chen, Y., Forouhar, F., Edstrom, W., Benach, J., Vorobiev, S., Acton, T., Shastry, R., Ma, L.-C., Xia, R., Montelione, G., Tong, L., Hunt, J., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.284 (Depositor), 0.296 (DCC)
R-Value Work:
0.238 (Depositor), 0.250 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

X-ray Structure of Dephospho-CoA Kinase from E. coli Norteast Structural Genomics Consortium Target ER57

Kuzin, A.P., Chen, Y., Forouhar, F., Edstrom, W., Benach, J., Vorobiev, S., Acton, T., Shastry, R., Ma, L.-C., Xia, R., Montelione, G., Tong, L., Hunt, J.

To be published.

Macromolecule Content

Total Structure Weight: 71.77 kDa
Atom Count: 4,803
Modelled Residue Count: 601
Deposited Residue Count: 642
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dephospho-CoA kinase	A, B, C	214	Escherichia coli	Mutation(s): 3 EC: 2.7.1.24
UniProt
Find proteins for P0A6I9 (Escherichia coli (strain K12)) Explore P0A6I9 Go to UniProtKB: P0A6I9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6I9
Sequence Annotations Expand
Reference Sequence LOADING

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 D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.284 (Depositor), 0.296 (DCC)
R-Value Work: 0.238 (Depositor), 0.250 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.63	α = 90
b = 80.905	β = 93.95
c = 75.454	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-05-11

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2004-05-11
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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X-ray Structure of Dephospho-CoA Kinase from E. coli Norteast Structural Genomics Consortium Target ER57

X-ray Structure of Dephospho-CoA Kinase from E. coli Norteast Structural Genomics Consortium Target ER57

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

1T3H | pdb_00001t3h