5V6D | pdb_00005v6d

Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate

PDB DOI: https://doi.org/10.2210/pdb5V6D/pdb

Classification: TRANSFERASE
Organism(s): Neisseria gonorrhoeae NCCP11945
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-16 Released: 2017-04-19
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.188 (Depositor), 0.189 (DCC)
R-Value Work:
0.150 (Depositor), 0.151 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5V6D

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate

Abendroth, J., Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 268.26 kDa
Atom Count: 20,042
Modeled Residue Count: 2,245
Deposited Residue Count: 2,384
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	149	Neisseria gonorrhoeae NCCP11945	Mutation(s): 0 Gene Names: ndk, NGK_1320 EC: 2.7.4.6
UniProt
Find proteins for B4RMG0 (Neisseria gonorrhoeae (strain NCCP11945)) Explore B4RMG0 Go to UniProtKB: B4RMG0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4RMG0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth G] SDF format, chain MA [auth J] SDF format, chain Q [auth A] SDF format, chain TA [auth M] SDF format, chain YA [auth O] SDF format, chain Y [auth D] SDF format, chain WA [auth N] SDF format, chain V [auth C] SDF format, chain T [auth B] SDF format, chain RA [auth L] SDF format, chain OA [auth K] SDF format, chain KA [auth I] SDF format, chain HA [auth H] SDF format, chain CA [auth F] SDF format, chain AB [auth P] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth G] MOL2 format, chain MA [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain TA [auth M] MOL2 format, chain YA [auth O] MOL2 format, chain Y [auth D] MOL2 format, chain WA [auth N] MOL2 format, chain V [auth C] MOL2 format, chain T [auth B] MOL2 format, chain RA [auth L] MOL2 format, chain OA [auth K] MOL2 format, chain KA [auth I] MOL2 format, chain HA [auth H] MOL2 format, chain CA [auth F] MOL2 format, chain AB [auth P] mmCIF format, chain AA [auth E] mmCIF format, chain EA [auth G] mmCIF format, chain MA [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain TA [auth M] mmCIF format, chain YA [auth O] mmCIF format, chain Y [auth D] mmCIF format, chain WA [auth N] mmCIF format, chain V [auth C] mmCIF format, chain T [auth B] mmCIF format, chain RA [auth L] mmCIF format, chain OA [auth K] mmCIF format, chain KA [auth I] mmCIF format, chain HA [auth H] mmCIF format, chain CA [auth F] mmCIF format, chain AB [auth P]	AA [auth E] AB [auth P] CA [auth F] EA [auth G] HA [auth H] AA [auth E], AB [auth P], CA [auth F], EA [auth G], HA [auth H], KA [auth I], MA [auth J], OA [auth K], Q [auth A], RA [auth L], T [auth B], TA [auth M], V [auth C], WA [auth N], Y [auth D], YA [auth O]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain AB [auth P] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain Q [auth A] Focus chain RA [auth L] Focus chain T [auth B] Focus chain TA [auth M] Focus chain V [auth C] Focus chain WA [auth N] Focus chain Y [auth D] Focus chain YA [auth O] Interactions & Density Focus chain AA [auth E] Focus chain AB [auth P] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain Q [auth A] Focus chain RA [auth L] Focus chain T [auth B] Focus chain TA [auth M] Focus chain V [auth C] Focus chain WA [auth N] Focus chain Y [auth D] Focus chain YA [auth O]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BB [auth P] SDF format, chain GA [auth H] SDF format, chain U [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain ZA [auth O] SDF format, chain Z [auth D] SDF format, chain XA [auth N] SDF format, chain VA [auth M] SDF format, chain UA [auth M] SDF format, chain SA [auth L] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain QA [auth K] SDF format, chain PA [auth K] SDF format, chain NA [auth J] SDF format, chain LA [auth I] SDF format, chain JA [auth H] SDF format, chain IA [auth H] SDF format, chain FA [auth G] SDF format, chain DA [auth F] SDF format, chain BA [auth E] MOL2 format, chain BB [auth P] MOL2 format, chain GA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain ZA [auth O] MOL2 format, chain Z [auth D] MOL2 format, chain XA [auth N] MOL2 format, chain VA [auth M] MOL2 format, chain UA [auth M] MOL2 format, chain SA [auth L] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth K] MOL2 format, chain PA [auth K] MOL2 format, chain NA [auth J] MOL2 format, chain LA [auth I] MOL2 format, chain JA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain DA [auth F] MOL2 format, chain BA [auth E] mmCIF format, chain BB [auth P] mmCIF format, chain GA [auth H] mmCIF format, chain U [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain ZA [auth O] mmCIF format, chain Z [auth D] mmCIF format, chain XA [auth N] mmCIF format, chain VA [auth M] mmCIF format, chain UA [auth M] mmCIF format, chain SA [auth L] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth K] mmCIF format, chain PA [auth K] mmCIF format, chain NA [auth J] mmCIF format, chain LA [auth I] mmCIF format, chain JA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain DA [auth F] mmCIF format, chain BA [auth E]	BA [auth E] BB [auth P] DA [auth F] FA [auth G] GA [auth H] BA [auth E], BB [auth P], DA [auth F], FA [auth G], GA [auth H], IA [auth H], JA [auth H], LA [auth I], NA [auth J], PA [auth K], QA [auth K], R [auth A], S [auth A], SA [auth L], U [auth B], UA [auth M], VA [auth M], W [auth C], X [auth C], XA [auth N], Z [auth D], ZA [auth O]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain BB [auth P] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain NA [auth J] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth L] Focus chain U [auth B] Focus chain UA [auth M] Focus chain VA [auth M] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth N] Focus chain Z [auth D] Focus chain ZA [auth O] Interactions & Density Focus chain BA [auth E] Focus chain BB [auth P] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain NA [auth J] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth L] Focus chain U [auth B] Focus chain UA [auth M] Focus chain VA [auth M] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth N] Focus chain Z [auth D] Focus chain ZA [auth O]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.188 (Depositor), 0.189 (DCC)
R-Value Work: 0.150 (Depositor), 0.151 (DCC)
R-Value Observed: 0.150 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.24	α = 104.31
b = 112.35	β = 98.5
c = 112.87	γ = 105.39

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-04-19

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-04-19
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

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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.