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- PDB-1iji: Crystal Structure of L-Histidinol Phosphate Aminotransferase with PLP -

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Basic information

Entry
Database: PDB / ID: 1iji
TitleCrystal Structure of L-Histidinol Phosphate Aminotransferase with PLP
ComponentsHistidinol Phosphate Aminotransferase
KeywordsTRANSFERASE / Aminotransferase / HisC / Histidine biosynthesis / Pyridoxal Phosphate
Function / homology
Function and homology information


histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
Histidinol-phosphate aminotransferase family / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Histidinol-phosphate aminotransferase family / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSivaraman, J. / Li, Y. / Larocque, R. / Schrag, J.D. / Cygler, M. / Matte, A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of histidinol phosphate aminotransferase (HisC) from Escherichia coli, and its covalent complex with pyridoxal-5'-phosphate and l-histidinol phosphate.
Authors: Sivaraman, J. / Li, Y. / Larocque, R. / Schrag, J.D. / Cygler, M. / Matte, A.
History
DepositionApr 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidinol Phosphate Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6412
Polymers39,3941
Non-polymers2471
Water2,342130
1
A: Histidinol Phosphate Aminotransferase
hetero molecules

A: Histidinol Phosphate Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2824
Polymers78,7882
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area7540 Å2
ΔGint-26 kcal/mol
Surface area25550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.857, 62.602, 45.273
Angle α, β, γ (deg.)90.00, 104.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histidinol Phosphate Aminotransferase / L-HISTIDINOL-PHOSPHATE AMINOTRANSFERASE / IMIDAZOLE ACETOL-PHOSPHATE TRANSAMINASE


Mass: 39393.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: P06986, histidinol-phosphate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, Tris HCl, Mgcl2, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMTris-HCl1drop
3200 mM1dropKCl
41 mMEDTA1drop
522.5 %(w/v)PEG33501reservoir
650 mMTris-HCl1reservoir
7200 mM1reservoirMgCl2
87 %(w/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. all: 40644 / Num. obs: 16911 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.199 / % possible all: 51
Reflection
*PLUS
Num. measured all: 40644

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1647 -RANDOM
Rwork0.213 ---
all-40644 --
obs-37811 89.3 %-
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 15 130 2854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 180 10.3 %
Rwork0.326 1570 -
obs--57.5 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 45 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.326

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