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- PDB-1bjw: ASPARTATE AMINOTRANSFERASE FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1bjw
TitleASPARTATE AMINOTRANSFERASE FROM THERMUS THERMOPHILUS
ComponentsASPARTATE AMINOTRANSFERASEAspartate transaminase
KeywordsAMINOTRANSFERASE / PYRIDOXAL ENZYME / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


aspartate-prephenate aminotransferase / aspartate-prephenate aminotransferase activity / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
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 ...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
PHOSPHATE ION / Aspartate/prephenate aminotransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 1.8 Å
AuthorsNakai, T. / Okada, K. / Kuramitsu, S. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochemistry / Year: 1999
Title: Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate.
Authors: Nakai, T. / Okada, K. / Akutsu, S. / Miyahara, I. / Kawaguchi, S. / Kato, R. / Kuramitsu, S. / Hirotsu, K.
History
DepositionJun 30, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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

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Assembly

Deposited unit
A: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2814
Polymers84,0912
Non-polymers1902
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-27 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.600, 113.860, 124.400
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 / Aspartate transaminase


Mass: 42045.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / Strain (production host): AB1157 / References: UniProt: Q56232, aspartate transaminase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.57 Å3/Da / Density % sol: 52.55 %
Crystal growpH: 4.3 / Details: pH 4.3
Crystal grow
*PLUS
Temperature: 293 K / pH: 7 / Method: vapor diffusion, hanging drop / Details: Nakai, T., (1998) Acta Crystallogr. D54, 1032.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mM1dropKCl
32 mMHEPES1drop
4300 mMammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1998 / Details: MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 74202 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.8 / % possible all: 0.235
Reflection
*PLUS
Num. measured all: 149097

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 1.8→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 7312 10 %RANDOM
Rwork0.215 ---
obs0.215 72271 89.5 %-
Displacement parametersBiso mean: 16.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5920 0 10 308 6238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.56
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.461.5
X-RAY DIFFRACTIONx_mcangle_it3.112
X-RAY DIFFRACTIONx_scbond_it2.232
X-RAY DIFFRACTIONx_scangle_it4.922.5
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2987 865 10 %
Rwork0.2898 7619 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.PLPTOPHCSDX.PRO
X-RAY DIFFRACTION3PARAM.PO4
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_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.56

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