3GR3 | pdb_00003gr3

Crystal structure of a nitroreductase-like family protein (pnba, bh06130) from bartonella henselae str. houston-1 at 1.45 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.170 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3GR3

Ligand Structure Quality Assessment 


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

Literature

Crystal structure of nitroreductase-like family protein (YP_033442.1) from BARTONELLA HENSELAE HOUSTON-1 at 1.45 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 55.02 kDa 
  • Atom Count: 4,558 
  • Modeled Residue Count: 452 
  • Deposited Residue Count: 460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitroreductase
A, B
230Bartonella henselae str. Houston-1Mutation(s): 0 
Gene Names: BH06130, pnbA, YP_033442.1
UniProt
Find proteins for A0A0H3M323 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1))
Explore A0A0H3M323 
Go to UniProtKB:  A0A0H3M323
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3M323
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN


Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
M [auth B]
N [auth B]
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
I [auth A],
Q [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL


Download:Ideal Coordinates CCD File
E [auth A],
L [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL

Query on UNL


Download:Ideal Coordinates CCD File
D [auth A],
K [auth B]		Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.170 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.064α = 90
b = 94.778β = 90
c = 103.945γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-11-27
    Changes: Data collection, Structure summary