3BHQ

CRYSTAL STRUCTURE OF A PUTATIVE TETR-FAMILY TRANSCRIPTIONAL REGULATOR (MLR_4833) FROM MESORHIZOBIUM LOTI MAFF303099 AT 1.54 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3BHQ/pdb

Classification: TRANSCRIPTION
Organism(s): Mesorhizobium japonicum MAFF 303099
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-28 Released: 2007-12-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.194
R-Value Work: 0.173
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of TetR-family transcriptional regulator (NP_105615.1) from Mesorhizobium loti at 1.54 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 48.71 kDa
Atom Count: 3,817
Modelled Residue Count: 404
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B	211	Mesorhizobium japonicum MAFF 303099	Mutation(s): 0 Gene Names: NP_105615.1, mlr4833
UniProt
Find proteins for Q98D70 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98D70 Go to UniProtKB: Q98D70
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q98D70
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 E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B]	C [auth A], D [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.194
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33BHQ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.534	α = 90
b = 64.221	β = 90
c = 142.613	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-11

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-12-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-09
Changes: Data collection, Structure summary