4WBT | pdb_00004wbt

Crystal structure of histidinol-phosphate aminotransferase from Sinorhizobium meliloti in complex with pyridoxal-5'-phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.163 (Depositor), 0.164 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Crystal structure of histidinol-phosphate aminotransferase from Sinorhizobium meliloti in complex with pyridoxal-5'-phosphate

Shabalin, I.G., Cooper, D.R., Minor, W.

To be published.

Macromolecule Content 

  • Total Structure Weight: 122.55 kDa 
  • Atom Count: 9,656 
  • Modeled Residue Count: 1,104 
  • Deposited Residue Count: 1,128 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable histidinol-phosphate aminotransferase
A, B, C
376Sinorhizobium meliloti 1021Mutation(s): 0 
Gene Names: hisC4, R01049, SMc02393
EC: 2.6.1.9
UniProt
Find proteins for Q92R63 (Rhizobium meliloti (strain 1021))
Explore Q92R63 
Go to UniProtKB:  Q92R63
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92R63
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4

Query on PE4


Download:Ideal Coordinates CCD File
M [auth C]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
PLP

Query on PLP


Download:Ideal Coordinates CCD File
D [auth A],
I [auth B],
L [auth C]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
PGE

Query on PGE


Download:Ideal Coordinates CCD File
K [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG


Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
J [auth B]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A, B, C
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.163 (Depositor), 0.164 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.055α = 90
b = 64.322β = 93.24
c = 137.048γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-3000data collection
HKL-3000phasing
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2022-04-13
    Changes: Database references, Refinement description, Structure summary
  • Version 1.4: 2023-12-27
    Changes: Data collection, Refinement description