4TQT | pdb_00004tqt

Crystal structure of Dihydropyrimidinase from Brucella suis

PDB DOI: https://doi.org/10.2210/pdb4TQT/pdb

Classification: HYDROLASE
Organism(s): Brucella suis 1330
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-06-12 Released: 2014-08-06
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.182 (Depositor), 0.180 (DCC)
R-Value Work:
0.135 (Depositor), 0.140 (DCC)
R-Value Observed:
0.137 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Dihydropyrimidinase from Brucella suis

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Davies, D.R., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 330.78 kDa
Atom Count: 23,274
Modeled Residue Count: 2,869
Deposited Residue Count: 2,982
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-hydantoinase	A, B, C, D, E A, B, C, D, E, F	497	Brucella suis 1330	Mutation(s): 0 Gene Names: dhT, BR0278, BS1330_I0279 EC: 3.5.2.2
UniProt
Find proteins for A0A0H3G9X2 (Brucella suis biovar 1 (strain 1330)) Explore A0A0H3G9X2 Go to UniProtKB: A0A0H3G9X2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3G9X2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain KA [auth F] SDF format, chain LA [auth F] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain LA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain LA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	EA [auth E] FA [auth E] G [auth A] H [auth A] KA [auth F] EA [auth E], FA [auth E], G [auth A], H [auth A], KA [auth F], LA [auth F], N [auth B], O [auth B], S [auth C], T [auth C], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] GA [auth E] AA [auth D], BA [auth D], CA [auth D], DA [auth D], GA [auth E], HA [auth E], I [auth A], IA [auth E], J [auth A], JA [auth E], K [auth A], L [auth A], M [auth A], MA [auth F], NA [auth F], OA [auth F], P [auth B], PA [auth F], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.182 (Depositor), 0.180 (DCC)
R-Value Work: 0.135 (Depositor), 0.140 (DCC)
R-Value Observed: 0.137 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34TQT

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.69	α = 90
b = 88.83	β = 91.17
c = 221.24	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2017-11-22
Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection