4WBT

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

PDB DOI: https://doi.org/10.2210/pdb4WBT/pdb

Classification: TRANSFERASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-09-03 Released: 2014-09-24
Deposition Author(s): Shabalin, I.G., Bacal, P., Kowalska, A.K., Cooper, D.R., Stead, M., Hammonds, J., Ahmed, M., Hillerich, B.S., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.163
R-Value Work: 0.146
R-Value Observed: 0.147

wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 1,104
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable histidinol-phosphate aminotransferase	A, B, C	376	Sinorhizobium meliloti 1021	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92R63
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE4 Query on PE4 Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C]	M [auth C]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C]	D [auth A], I [auth B], L [auth C]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B]	F [auth A], G [auth A], H [auth A], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX Query on CSX	A, B, C	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.163
R-Value Work: 0.146
R-Value Observed: 0.147
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/M3B88T

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.055	α = 90
b = 64.322	β = 93.24
c = 137.048	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	data collection
HKL-3000	phasing
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Funding Organization	Location	Grant 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

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4WBT

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)