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- PDB-1gex: CRYSTAL STRUCTURE OF HISTIDINOL-PHOSPHATE AMINOTRANSFERASE COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1gex
TitleCRYSTAL STRUCTURE OF HISTIDINOL-PHOSPHATE AMINOTRANSFERASE COMPLEXED WITH HISTIDINOL-PHOSPHATE
ComponentsHISTIDINOL-PHOSPHATE AMINOTRANSFERASE
KeywordsTRANSFERASE / alpha/beta-structure / Aminotransferase / PYRIDOXAL-5'-PHOSPHATE / PHOSPHORIC ACID MONO-[2-AMINO-3-(3H-IMIDAZOL-4-YL)-PROPYL]ESTER / complex
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
Chem-HSA / PYRIDOXAL-5'-PHOSPHATE / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsHaruyama, K. / Nakai, T. / Miyahara, I. / Hirotsu, K. / Mizuguchi, H. / Hayashi, H. / Kagamiyama, H.
CitationJournal: Biochemistry / Year: 2001
Title: Structures of Escherichia coli histidinol-phosphate aminotransferase and its complexes with histidinol-phosphate and N-(5'-phosphopyridoxyl)-L-glutamate: double substrate recognition of the enzyme.
Authors: Haruyama, K. / Nakai, T. / Miyahara, I. / Hirotsu, K. / Mizuguchi, H. / Hayashi, H. / Kagamiyama, H.
History
DepositionNov 30, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8623
Polymers39,3941
Non-polymers4682
Water2,162120
1
A: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules

A: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7256
Polymers78,7882
Non-polymers9374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8460 Å2
ΔGint-35 kcal/mol
Surface area24080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.924, 63.836, 46.365
Angle α, β, γ (deg.)90.00, 104.06, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein HISTIDINOL-PHOSPHATE AMINOTRANSFERASE


Mass: 39393.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HISC / Plasmid: PUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
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: Chemical ChemComp-HSA / PHOSPHORIC ACID MONO-[2-AMINO-3-(3H-IMIDAZOL-4-YL)-PROPYL]ESTER


Mass: 221.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N3O4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PEG 4000, magnesium chloride, tris, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-25 mg/mlprotein1drop
217.5 %(w/v)PEG40001reservoir
382 mmHsp1reservoir
4200 mM1reservoirMgCl2
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 25, 1999
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 18942 / Num. obs: 18942 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.231 / Num. unique all: 1811 / % possible all: 95.5
Reflection
*PLUS
Num. measured all: 87507
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 942 -RANDOM
Rwork0.191 ---
all0.197 18520 --
obs0.195 18299 97.2 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 29 120 2789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.411
X-RAY DIFFRACTIONx_torsion_deg24.32
X-RAY DIFFRACTIONx_torsion_impr_deg1.225
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.335 / Rfactor Rwork: 0.285

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