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- PDB-1fg7: CRYSTAL STRUCTURE OF L-HISTIDINOL PHOSPHATE AMINOTRANSFERASE WITH... -

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Basic information

Entry
Database: PDB / ID: 1fg7
TitleCRYSTAL STRUCTURE OF L-HISTIDINOL PHOSPHATE AMINOTRANSFERASE WITH PYRIDOXAL-5'-PHOSPHATE
ComponentsHISTIDINOL PHOSPHATE AMINOTRANSFERASE
KeywordsTRANSFERASE / Aminotransferase / HisC / Histidine Biosynthesis / Pyridoxal Phosphate / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsSivaraman, J. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
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
DepositionJul 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 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 / Item: _software.classification / _software.name
Revision 1.4Oct 16, 2024Group: 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 / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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)39,8302
Polymers39,5821
Non-polymers2481
Water4,035224
1
A: HISTIDINOL PHOSPHATE AMINOTRANSFERASE
hetero molecules

A: HISTIDINOL PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6594
Polymers79,1632
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area7660 Å2
ΔGint-29 kcal/mol
Surface area25040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.168, 62.575, 45.284
Angle α, β, γ (deg.)90.00, 104.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HISTIDINOL PHOSPHATE AMINOTRANSFERASE / IMIDAZOLE ACETOL-PHOSPHATE TRANSAMINASE


Mass: 39581.562 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)
References: UniProt: P06986, histidinol-phosphate transaminase
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.35 %
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: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.961123
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Mar 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961123 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 504180 / Num. obs: 137314 / % possible obs: 99.1 % / Observed criterion σ(I): 0.3 / Redundancy: 4 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4 % / Rmerge(I) obs: 0.251 / Num. unique all: 13543 / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 504180

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
Adxvdata processing
SCALEPACKdata scaling
RefinementResolution: 1.5→45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.219 2720 RANDOM
Rwork0.205 --
obs-110600 -
Refinement stepCycle: LAST / Resolution: 1.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 16 224 2957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_d23.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 45 Å / σ(F): 0 / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.5

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