5VRB | pdb_00005vrb

Crystal structure of a transketolase from Neisseria gonorrhoeae

PDB DOI: https://doi.org/10.2210/pdb5VRB/pdb

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

Deposited: 2017-05-10 Released: 2017-05-17
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:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.150 (Depositor), 0.150 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a transketolase from Neisseria gonorrhoeae

Edwards, T.E., Delker, S.L., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 291.78 kDa
Atom Count: 21,287
Modeled Residue Count: 2,528
Deposited Residue Count: 2,668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase	A, B, C, D	667	Neisseria gonorrhoeae NCCP11945	Mutation(s): 0 Gene Names: NGK_0759 EC: 2.2.1.1
UniProt
Find proteins for B4RKU9 (Neisseria gonorrhoeae (strain NCCP11945)) Explore B4RKU9 Go to UniProtKB: B4RKU9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4RKU9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain E [auth A]	E [auth A] L [auth C] M [auth C] Q [auth D] R [auth D] E [auth A], L [auth C], M [auth C], Q [auth D], R [auth D], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth B] J [auth B] F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], N [auth C], O [auth C], P [auth C], T [auth D], U [auth D], V [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on OCS	A, B, C, D	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.191 (Depositor), 0.190 (DCC)
R-Value Work: 0.150 (Depositor), 0.150 (DCC)
R-Value Observed: 0.151 (Depositor)

Diffraction Data: https://doi.org/10.18430/M35VRB

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.45	α = 90
b = 114.21	β = 90.11
c = 125.69	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-05-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-05-17
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection