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- PDB-1ajs: REFINEMENT AND COMPARISON OF THE CRYSTAL STRUCTURES OF PIG CYTOSO... -

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Basic information

Entry
Database: PDB / ID: 1ajs
TitleREFINEMENT AND COMPARISON OF THE CRYSTAL STRUCTURES OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE AND ITS COMPLEX WITH 2-METHYLASPARTATE
Components(ASPARTATE AMINOTRANSFERASE) x 2
KeywordsAMINOTRANSFERASE / CYTOSOLIC ASPARTATE AMINOTRANSFERASE / PIG / IN THE PRESENCE OF LIGAND 2-METHYLASPARTATE
Function / homology
Function and homology information


Aspartate and asparagine metabolism / Malate-aspartate shuttle / L-glutamate catabolic process to aspartate / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / glycerol biosynthetic process ...Aspartate and asparagine metabolism / Malate-aspartate shuttle / L-glutamate catabolic process to aspartate / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process / glutamate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / 2-oxoglutarate metabolic process / fatty acid homeostasis / Notch signaling pathway / response to glucocorticoid / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / 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
Chem-PLA / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / ISOMORPHOUS DIFFERENCE MAP / Resolution: 1.6 Å
AuthorsRhee, S. / Silva, M.M. / Hyde, C.C. / Rogers, P.H. / Metzler, C.M. / Metzler, D.E. / Arnone, A.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: Refinement and comparisons of the crystal structures of pig cytosolic aspartate aminotransferase and its complex with 2-methylaspartate.
Authors: Rhee, S. / Silva, M.M. / Hyde, C.C. / Rogers, P.H. / Metzler, C.M. / Metzler, D.E. / Arnone, A.
#1: Journal: Transaminases / Year: 1985
Title: Pig Cytosolic Aspartate Aminotransferase
Authors: Arnone, A. / Rogers, P.H. / Hyde, C.C. / Briley, P.D. / Metzler, C.M. / Metzler, D.E.
History
DepositionMay 8, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3933
Polymers93,0152
Non-polymers3781
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-18 kcal/mol
Surface area30020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.000, 130.800, 55.800
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: 46393.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE COENZYME PYRIDOXAL 5'-PHOSPHATE IN SUBUNIT A FORMS A SCHIFF BASE WITH THE SUBSTRATE ANALOG 2-METHYLASPARTATE, AND FORMS THE EXTERNAL ALDIMINE. BUT DUE TO CRYSTAL LATTICE PACKINGS THE ...Details: THE COENZYME PYRIDOXAL 5'-PHOSPHATE IN SUBUNIT A FORMS A SCHIFF BASE WITH THE SUBSTRATE ANALOG 2-METHYLASPARTATE, AND FORMS THE EXTERNAL ALDIMINE. BUT DUE TO CRYSTAL LATTICE PACKINGS THE COENZYME IN SUBUNIT B IS STILL IN THE INTERNAL ALDIMINE WITH THE SIDE CHAIN OF LYS 258.
Source: (natural) Sus scrofa (pig) / References: UniProt: P00503, aspartate transaminase
#2: Protein ASPARTATE AMINOTRANSFERASE


Mass: 46621.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE COENZYME PYRIDOXAL 5'-PHOSPHATE IN SUBUNIT A FORMS A SCHIFF BASE WITH THE SUBSTRATE ANALOG 2-METHYLASPARTATE, AND FORMS THE EXTERNAL ALDIMINE. BUT DUE TO CRYSTAL LATTICE PACKINGS THE ...Details: THE COENZYME PYRIDOXAL 5'-PHOSPHATE IN SUBUNIT A FORMS A SCHIFF BASE WITH THE SUBSTRATE ANALOG 2-METHYLASPARTATE, AND FORMS THE EXTERNAL ALDIMINE. BUT DUE TO CRYSTAL LATTICE PACKINGS THE COENZYME IN SUBUNIT B IS STILL IN THE INTERNAL ALDIMINE WITH THE SIDE CHAIN OF LYS 258.
Source: (natural) Sus scrofa (pig) / References: UniProt: P00503, aspartate transaminase
#3: Chemical ChemComp-PLA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID / N-PYRIDOXYL-2-METHYLASPARTIC ACID-5-MONOPHOSPHATE


Mass: 378.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N2O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 48 %
Crystal growpH: 5.4 / Details: 40MM SODIUM ACETATE (PH 5.4)/8% PEG6000
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 %PEG60001reservoir
240 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 1, 1990
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 114162 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 16.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→1.73 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.197 / % possible all: 69.9
Reflection
*PLUS
Num. measured all: 476759 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 69.9 % / Rmerge(I) obs: 0.197

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Processing

Software
NameVersionClassification
SEEMANUSCRIPTmodel building
PROLSQrefinement
UCSDdata reduction
FROMUCSDdata scaling
RefinementMethod to determine structure: ISOMORPHOUS DIFFERENCE MAP / Resolution: 1.6→8 Å / σ(F): 2 /
RfactorNum. reflection% reflection
obs0.173 108895 90.6 %
Displacement parametersBiso mean: 22.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6546 0 42 325 6913
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.01
X-RAY DIFFRACTIONp_angle_d0.0280.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.52.5
X-RAY DIFFRACTIONp_mcangle_it3.83.8
X-RAY DIFFRACTIONp_scbond_it7.67.6
X-RAY DIFFRACTIONp_scangle_it11.211.2
X-RAY DIFFRACTIONp_plane_restr0.0140.014
X-RAY DIFFRACTIONp_chiral_restr0.1560.08
X-RAY DIFFRACTIONp_singtor_nbd0.170.2
X-RAY DIFFRACTIONp_multtor_nbd0.1680.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1560.2
X-RAY DIFFRACTIONp_planar_tor4.45
X-RAY DIFFRACTIONp_staggered_tor18.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.725
X-RAY DIFFRACTIONp_special_tor

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