2PKH

Structural Genomics, the crystal structure of the C-terminal domain of histidine utilization repressor from Pseudomonas syringae pv. tomato str. DC3000

PDB DOI: https://doi.org/10.2210/pdb2PKH/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Pseudomonas syringae pv. tomato str. DC3000
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2007-04-17 Released: 2007-05-15
Deposition Author(s): Tan, K., Zhou, M., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.277
R-Value Work: 0.219
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of the C-terminal domain of histidine utilization repressor from Pseudomonas syringae pv. tomato str. DC3000.

Tan, K., Zhou, M., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 136.74 kDa
Atom Count: 10,115
Modelled Residue Count: 1,132
Deposited Residue Count: 1,184
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine utilization repressor	A, B, C, D, E A, B, C, D, E, F, G, H	148	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 2 Gene Names: hutC, PSPTO5172
UniProt
Find proteins for Q87UX0 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q87UX0 Go to UniProtKB: Q87UX0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87UX0
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.277
R-Value Work: 0.219
R-Value Observed: 0.222
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.845	α = 90
b = 100.955	β = 90
c = 130.187	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-15

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-05-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary