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- PDB-1cq6: ASPARTATE AMINOTRANSFERASE COMPLEX WITH C4-PYRIDOXAL-5P-PHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1cq6
TitleASPARTATE AMINOTRANSFERASE COMPLEX WITH C4-PYRIDOXAL-5P-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
2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.7 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 6, 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)43,9532
Polymers43,6191
Non-polymers3341
Water1,964109
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9074
Polymers87,2382
Non-polymers6692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6430 Å2
ΔGint-26 kcal/mol
Surface area29480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.15, 86.32, 79.24
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-PY4 / 2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID / VITAMIN B6 COMPLEXED WITH 2-AMINO-BUTYRIC ACID


Mass: 334.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, potassium phosphate, C4-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

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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: Sep 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14620 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 59.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.22 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 79877

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 2.7→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.297 1413 RANDOM
Rwork0.241 --
obs-14301 -
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 22 109 3200
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.241 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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