1TO6 | pdb_00001to6

Glycerate kinase from Neisseria meningitidis (serogroup A)

PDB DOI: https://doi.org/10.2210/pdb1TO6/pdb

Classification: TRANSFERASE
Organism(s): Neisseria meningitidis serogroup A
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-06-13 Released: 2004-06-22
Deposition Author(s): Rajashankar, K.R., Kniewel, R., Solorzano, V., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.283 (Depositor), 0.233 (DCC)
R-Value Work:
0.226 (Depositor), 0.228 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1TO6

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

Literature

Glycerate kinase from Neisseria meningitidis (serogroup A)

RAJASHANKAR, K.R., KNIEWEL, R., SOLORZANO, V., LIMA, C.D.

To be published.

Macromolecule Content

Total Structure Weight: 79.71 kDa
Atom Count: 5,777
Modeled Residue Count: 742
Deposited Residue Count: 742
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerate kinase	A, B	371	Neisseria meningitidis serogroup A	Mutation(s): 0 Gene Names: GLXK, NMA1473 EC: 2.7.1.31
UniProt
Find proteins for P57098 (Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 / Z2491)) Explore P57098 Go to UniProtKB: P57098
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P57098
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 E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth B] C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.283 (Depositor), 0.233 (DCC)
R-Value Work: 0.226 (Depositor), 0.228 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.767	α = 90
b = 77.386	β = 107.41
c = 101.436	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-06-22

Deposition Author(s):

Rajashankar, K.R.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-06-22
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: 2021-02-03
Changes: Derived calculations, Structure summary
Version 1.4: 2024-02-14
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.