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- PDB-1c9c: ASPARTATE AMINOTRANSFERASE COMPLEXED WITH C3-PYRIDOXAL-5'-PHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1c9c
TitleASPARTATE AMINOTRANSFERASE COMPLEXED WITH C3-PYRIDOXAL-5'-PHOSPHATE
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsTRANSFERASE / ENZYME-SUBSTRATE COMPLEX
Function / homology
Function and homology information


L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I 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
ALANYL-PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsIshijima, J. / Nakai, T. / Kawaguchi, S. / Hirotsu, K. / Kuramitsu, S.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Free energy requirement for domain movement of an enzyme
Authors: Ishijima, J. / Nakai, T. / Kawaguchi, S. / Hirotsu, K. / Kuramitsu, S.
History
DepositionAug 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9392
Polymers43,6191
Non-polymers3201
Water2,108117
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8794
Polymers87,2382
Non-polymers6402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6360 Å2
ΔGint-24 kcal/mol
Surface area29190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)156.98, 87.27, 79.73
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
DetailsTHE FUNCTIONAL DIMER CAN BE GENERATED BY APPLYING THE SYMMETRY OPERATOR (X, -Y, -Z) TO THE ATOMIC COORDINATES PRESENTED IN THIS ENTRY.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 43619.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase
#2: Chemical ChemComp-PP3 / ALANYL-PYRIDOXAL-5'-PHOSPHATE / PYRIDOXYL-ALANINE-5-PHOSPHATE / VITAMIN B6 COMPLEXED WITH ALANINE


Mass: 320.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, potassium phosphate, C3-pyridoxal-5p-phosphate, sodium azide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mg/mlprotein1drop
210 mMpotassium phosphate1drop
30.010 mMPLP-amino acid1drop
40.3 mM1droppH8.0NaN3
535 %satammonium sulfate1reservoir
610 mMpotassium phosphate1reservoir
70.3 mM1reservoirpH8.0NaN3

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 104038 / Num. obs: 19863 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.22 / Num. unique all: 1947 / % possible all: 90.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 77327

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 2.4→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.269 1927 RANDOM
Rwork0.202 --
obs-19586 -
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 21 117 3207
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor obs: 0.202 / Rfactor Rfree: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS

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