1S96 | pdb_00001s96

The 2.0 A X-ray structure of Guanylate Kinase from E.coli

PDB DOI: https://doi.org/10.2210/pdb1S96/pdb

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

Deposited: 2004-02-03 Released: 2004-02-10
Deposition Author(s): Kreusch, A., Spraggon, G., Klock, H.E., McMullan, D., Vincent, J., Rodrigues, K., Lesley, S.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.247 (Depositor)
R-Value Work:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Structure of Guanylate Kinase from Escherichia coli at 2.0 A resolution

Kreusch, A., Spraggon, G., Klock, H.E., McMullan, D., Vincent, J., Rodrigues, K., Lesley, S.A.

To be published.

Macromolecule Content

Total Structure Weight: 51.02 kDa
Atom Count: 3,611
Modeled Residue Count: 409
Deposited Residue Count: 438
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate kinase	A, B	219	Escherichia coli	Mutation(s): 6 Gene Names: GMK, SPOR, B3648, C4473, SF3688, S4081 EC: 2.7.4.8
UniProt
Find proteins for P60546 (Escherichia coli (strain K12)) Explore P60546 Go to UniProtKB: P60546
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60546
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain E [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247 (Depositor)
R-Value Work: 0.195 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.552	α = 90
b = 124.552	β = 90
c = 124.552	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-02-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-02-10
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary

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Deposit Data

Help and Resources

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The 2.0 A X-ray structure of Guanylate Kinase from E.coli

The Structure of Guanylate Kinase from Escherichia coli at 2.0 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

1S96 | pdb_00001s96