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- PDB-1oat: ORNITHINE AMINOTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1oat
TitleORNITHINE AMINOTRANSFERASE
ComponentsORNITHINE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / PLP-DEPENDENT ENZYME / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, NON-CRYSTALLOGRAPHIC AVERAGING / Resolution: 2.5 Å
AuthorsShen, B.W. / Schirmer, T. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of human recombinant ornithine aminotransferase.
Authors: Shen, B.W. / Hennig, M. / Hohenester, E. / Jansonius, J.N. / Schirmer, T.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Recombinant Human Ornithine Aminotransferase
Authors: Shen, B.W. / Ramesh, V. / Mueller, R. / Hohenester, E. / Hennig, M. / Jansonius, J.N.
History
DepositionMar 26, 1997Processing site: BNL
Revision 1.0Apr 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 14, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status ...diffrn_source / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Jul 21, 2021Group: Derived calculations / Refinement description / Category: refine / struct_conn
Item: _refine.ls_percent_reflns_obs / _struct_conn.pdbx_leaving_atom_flag ..._refine.ls_percent_reflns_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.5Aug 9, 2023Group: Advisory / Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,5226
Polymers145,7813
Non-polymers7413
Water7,674426
1
A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6824
Polymers97,1872
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-61 kcal/mol
Surface area25800 Å2
MethodPISA, PQS
2
C: ORNITHINE AMINOTRANSFERASE
hetero molecules

C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6824
Polymers97,1872
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11570 Å2
ΔGint-62 kcal/mol
Surface area25720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.300, 116.300, 190.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.8981, 0.0607, -0.4356), (0.0652, -0.9979, -0.0047), (-0.4349, -0.0242, -0.9001)8, 73.8, 45.33
2given(-0.4374, -0.8721, 0.2192), (0.771, -0.4892, -0.4077), (0.4628, -0.0093, 0.8864)72.75, 39.41, 6.73

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Components

#1: Protein ORNITHINE AMINOTRANSFERASE


Mass: 48593.668 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Plasmid: PASK40 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83 / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.78 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal
*PLUS
Density % sol: 51.9 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
250 mMTris-HCl1drop
30.01 MPLP1drop
410-15 %(w/v)PEG60001reservoir
550-200 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Oct 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 52220 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.082
Reflection shellRedundancy: 5.6 % / Rmerge(I) obs: 0.35 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 38 Å
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.349

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MARXDSdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, NON-CRYSTALLOGRAPHIC AVERAGING
Starting model: DIALKYLGLYCINE DECARBOXYLASE, PDB ENTRY 1DGD

1dgd


Resolution: 2.5→38 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.235 -10 %RANDOM
Rwork0.185 ---
obs0.185 49620 95.3 %-
Displacement parametersBiso mean: 19.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9483 0 45 426 9954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.2
X-RAY DIFFRACTIONx_mcangle_it6.4
X-RAY DIFFRACTIONx_scbond_it5.4
X-RAY DIFFRACTIONx_scangle_it8
LS refinement shellResolution: 2.5→2.53 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.344 -10 %
Rwork0.191 1481 -
obs--95.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.171 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.58
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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