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

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Basic information

Entry
Database: PDB / ID: 1ajr
TitleREFINEMENT AND COMPARISON OF THE CRYSTAL STRUCTURES OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE AND ITS COMPLEX WITH 2-METHYLASPARTATE
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / CYTOSOLIC ASPARTATE AMINOTRANSFERASE / PIG / HOMODIMER IN THE ABSENCE OF LIGAND
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
Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.74 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
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

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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


Theoretical massNumber of molelcules
Total (without water)93,2432
Polymers93,2432
Non-polymers00
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-19 kcal/mol
Surface area30560 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
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999731, 0.005529, 0.022518), (0.00327, -0.927823, 0.373005), (0.022955, 0.372978, 0.927556)
Vector: -82.75525, -48.24322, 10.722)

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 46621.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: LYS258 SIDE CHAIN FORMS THE SCHIFF BASE WITH COENZYME PYRIDOXAL 5'-PHOSPHATE
Source: (natural) Sus scrofa (pig) / References: UniProt: P00503, aspartate transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2

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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: 1.74→100 Å / Num. obs: 91745 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.054 / Net I/σ(I): 12.1
Reflection shellResolution: 1.74→1.87 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.17 / % possible all: 79.7
Reflection
*PLUS
Num. measured all: 444811 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 79.7 % / Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
SEEMANUSCRIPTmodel building
PROLSQrefinement
UCSDdata reduction
FROMUCSDdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.74→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.17 --
obs-88868 95 %
Displacement parametersBiso mean: 24.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.74→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 32 348 6932
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.01
X-RAY DIFFRACTIONp_angle_d0.0260.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.03
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_it7.27.2
X-RAY DIFFRACTIONp_scangle_it10.810.8
X-RAY DIFFRACTIONp_plane_restr0.0130.013
X-RAY DIFFRACTIONp_chiral_restr0.1450.08
X-RAY DIFFRACTIONp_singtor_nbd0.1680.2
X-RAY DIFFRACTIONp_multtor_nbd0.1710.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1630.2
X-RAY DIFFRACTIONp_planar_tor4.35
X-RAY DIFFRACTIONp_staggered_tor18.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.825
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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