8H8H | pdb_00008h8h

Crystal structure of the N-terminal domain of H-NS family protein TurB (TurB_nt50)

PDB DOI: https://doi.org/10.2210/pdb8H8H/pdb

Classification: TRANSCRIPTION
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-22 Released: 2022-11-09
Deposition Author(s): Vasileva, D., Suzuki-Minakuchi, C., Arakawa, T., Nojiri, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.285 (Depositor), 0.290 (DCC)
R-Value Work:
0.246 (Depositor), 0.250 (DCC)
R-Value Observed:
0.251 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the N-terminal domain of H-NS family protein TurB (TurB_nt50)

Vasileva, D., Suzuki-Minakuchi, C., Arakawa, T., Nojiri, H.

To be published.

Macromolecule Content

Total Structure Weight: 54.72 kDa
Atom Count: 3,255
Modeled Residue Count: 404
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-NS family protein MvaT	A, B, C, D, E A, B, C, D, E, F, G, H	58	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: PP_3765
UniProt
Find proteins for Q88GF9 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88GF9 Go to UniProtKB: Q88GF9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q88GF9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.285 (Depositor), 0.290 (DCC)
R-Value Work: 0.246 (Depositor), 0.250 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.692	α = 90
b = 63.303	β = 90
c = 275.872	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Suzuki-Minakuchi, C.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K05408
Japan Society for the Promotion of Science (JSPS)	Japan	21H02097
Japan Science and Technology	Japan	JPMJER1502

Revision History (Full details and data files)

Version 1.0: 2022-11-09
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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.