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- PDB-1yaa: ASPARTATE AMINOTRANSFERASE FROM SACCHAROMYCES CEREVISIAE CYTOPLASM -

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Basic information

Entry
Database: PDB / ID: 1yaa
TitleASPARTATE AMINOTRANSFERASE FROM SACCHAROMYCES CEREVISIAE CYTOPLASM
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / TRANSFERASE
Function / homology
Function and homology information


Aspartate and asparagine metabolism / Malate-aspartate shuttle / negative regulation of translation in response to oxidative stress / aspartate biosynthetic process / aspartate metabolic process / glutamate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / 2-oxoglutarate metabolic process / ribosomal large subunit binding ...Aspartate and asparagine metabolism / Malate-aspartate shuttle / negative regulation of translation in response to oxidative stress / aspartate biosynthetic process / aspartate metabolic process / glutamate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / 2-oxoglutarate metabolic process / ribosomal large subunit binding / pyridoxal phosphate binding / peroxisome / cytosol
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
MALEIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsJeffery, C.J.
Citation
Journal: Protein Sci. / Year: 1998
Title: Crystal structure of Saccharomyces cerevisiae cytosolic aspartate aminotransferase.
Authors: Jeffery, C.J. / Barry, T. / Doonan, S. / Petsko, G.A. / Ringe, D.
#1: Journal: To be Published
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Aspartate Aminotransferase from Saccharomyces Cerevisiae
Authors: Jeffery, C.J. / Barry, T. / Doonan, S. / Petsko, G.A. / Ringe, D.
History
DepositionJan 27, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _pdbx_database_status.process_site / _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: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
C: ASPARTATE AMINOTRANSFERASE
D: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,89912
Polymers181,4464
Non-polymers1,4538
Water12,899716
1
A: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4506
Polymers90,7232
Non-polymers7264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-28 kcal/mol
Surface area30020 Å2
MethodPISA
2
C: ASPARTATE AMINOTRANSFERASE
D: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4506
Polymers90,7232
Non-polymers7264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-27 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.310, 134.630, 98.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ASPARTATE AMINOTRANSFERASE


Mass: 45361.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: PYRIDOXAL PHOSPHATE COFACTOR COVALENTLY BOUND TO LYS 258 VIA SCHIFF BASE LINKAGE IN EACH SUBUNIT
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / References: UniProt: P23542, aspartate transaminase
#2: Chemical
ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4O4
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 4.6
Details: PROTEIN SOLUTION CONTAINED 5-15MG PROTEIN, 10MM PMSF, 10MM PLP, 10MM SODIUM ACETATE BUFFER, PH 5.8, AND 100MM MALEATE. RESERVOIR SOLUTION CONTAINED 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ...Details: PROTEIN SOLUTION CONTAINED 5-15MG PROTEIN, 10MM PMSF, 10MM PLP, 10MM SODIUM ACETATE BUFFER, PH 5.8, AND 100MM MALEATE. RESERVOIR SOLUTION CONTAINED 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE BUFFER, PH 4.6, AND 20-22% PEG 4000.
PH range: 4.6-5.8
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.8 / Method: vapor diffusion, hanging drop / Details: Jeffery, C.J., (1998) Acta Cryst., D54, 659.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-15 mg/mlprotein1drop
20.010 mMPMSF1drop
30.010 mMPLP1drop
410 mMsodium acetate1drop
50.100 mMsodium maleate1drop
60.2 Mammonium acetate1reservoir
70.1 Macetate1reservoir
822-20 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1992
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.05 Å / Num. obs: 470081 / % possible obs: 93 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.12 / Rsym value: 0.12
Reflection shellResolution: 2.05→2.14 Å / % possible all: 87
Reflection
*PLUS
Num. obs: 100347 / % possible obs: 93 % / Num. measured all: 470081
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CST

2cst


Resolution: 2.05→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 9617 10 %RANDOM
Rwork0.231 ---
obs0.231 100344 93 %-
Displacement parametersBiso mean: 19.9 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12788 0 92 716 13596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.05→2.14 Å / Rfactor Rfree error: 0.001 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.409 1062 10 %
Rwork0.348 10733 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27

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