7LUY | pdb_00007luy

Crystal Structure of guanylate kinase from Bartonella henselae str. Houston-1

PDB DOI: https://doi.org/10.2210/pdb7LUY/pdb

Classification: TRANSFERASE
Organism(s): Bartonella henselae str. Houston-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-02-23 Released: 2021-03-17
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.200 (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 guanylate kinase from Bartonella henselae str. Houston-1

Abendroth, J., Dranow, D.M., Sankaran, B., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 171.05 kDa
Atom Count: 9,673
Modeled Residue Count: 1,208
Deposited Residue Count: 1,458
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, C, D, E A, B, C, D, E, F	243	Bartonella henselae str. Houston-1	Mutation(s): 0 Gene Names: gmk, BH05390 EC: 2.7.4.8
UniProt
Find proteins for Q6G439 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1)) Explore Q6G439 Go to UniProtKB: Q6G439
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6G439
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] J [auth A] K [auth B] N [auth C] G [auth A], H [auth A], J [auth A], K [auth B], N [auth C], O [auth D], P [auth D], S [auth E], T [auth E], Y [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain Y [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain Y [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A] L [auth B] M [auth B] Q [auth D] R [auth D] I [auth A], L [auth B], M [auth B], Q [auth D], R [auth D], U [auth E], V [auth E], W [auth E], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (DCC)
R-Value Observed: 0.200 (Depositor)

Diffraction Data: https://doi.org/10.18430/m37luy

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.82	α = 90
b = 101.91	β = 115.982
c = 86.66	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-10-22
Changes: Structure summary