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- PDB-2oat: ORNITHINE AMINOTRANSFERASE COMPLEXED WITH 5-FLUOROMETHYLORNITHINE -

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Basic information

Entry
Database: PDB / ID: 2oat
TitleORNITHINE AMINOTRANSFERASE COMPLEXED WITH 5-FLUOROMETHYLORNITHINE
ComponentsORNITHINE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / 5-FLUOROMETHYLORNITHINE / 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
Chem-PFM / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER TECHNIQUES / Resolution: 1.95 Å
AuthorsStorici, P. / Schirmer, T.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of human ornithine aminotransferase complexed with the highly specific and potent inhibitor 5-fluoromethylornithine.
Authors: Storici, P. / Capitani, G. / Muller, R. / Schirmer, T. / Jansonius, J.N.
#1: 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.
#2: 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.
#3: Journal: Biochem.J. / Year: 1990
Title: Dl-Canaline and 5-Fluoromethylornithine. Comparison of Two Inactivators of Ornithine Aminotransferase
Authors: Bolkenius, F.N. / Knodgen, B. / Seiler, N.
History
DepositionMay 7, 1998Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)146,9046
Polymers145,7813
Non-polymers1,1233
Water13,403744
1
C: ORNITHINE AMINOTRANSFERASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)195,8728
Polymers194,3754
Non-polymers1,4974
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_555y,x,-z1
identity operation1_555x,y,z1
2
A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9364
Polymers97,1872
Non-polymers7492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-62 kcal/mol
Surface area25560 Å2
MethodPISA, PQS
3
C: ORNITHINE AMINOTRANSFERASE
hetero molecules

C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9364
Polymers97,1872
Non-polymers7492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12120 Å2
ΔGint-62 kcal/mol
Surface area25520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.280, 115.280, 186.810
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(0.8997, 0.0625, -0.432), (0.0625, -0.9979, -0.0142), (-0.432, -0.0142, -0.9018)7.6269, 73.1022, 44.1125
2given(-0.4449, 0.7768, 0.4458), (-0.8683, -0.496, -0.0024), (0.2192, -0.3881, 0.8951)-1.3448, 81.5594, -6.4618
DetailsTHERE ARE ONE AND A HALF DIMERS IN THE ASYMMETRIC UNIT. CHAINS A AND B REFER TO THE TWO SUBUNITS OF THE FIRST DIMER. CHAIN C REFERS TO ONE SUBUNIT OF THE SECOND DIMER; THE OTHER SUBUNIT IS RELATED BY CRYSTAL SYMMETRY.

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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) / Cellular location: INTRAMITOCHONDRIA / Gene: OAT / Organ: LIVER / Organelle: MITOCHONDRIA / Plasmid: PMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): TB1 / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical ChemComp-PFM / 1-AMINO-7-(2-METHYL-3-OXIDO-5-((PHOSPHONOXY)METHYL)-4-PYRIDOXAL-5-OXO-6-HEPTENATE / PYRIDOXYLIDENE-PROPEN-1-YL-3-ALANINE-5-PHOSPHATE


Mass: 374.283 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H19N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / 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: 2.65 Å3/Da / Density % sol: 50.9 %
Crystal growpH: 7.9
Details: (2S,5S)5FMORN-OAT WAS CO-CRYSTALLIZED FROM 6-10% PEG 6000, 1MM DTT, 120-160 MM NACL, 10-20% GLYCEROL, 50 MM TRICIN, PH 7.9.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16-10 %(v/v)PEG60001reservoir
21 mM1,4-dithiothreitol1reservoir
3120-160 mM1reservoirNaCl
450 mMTricin1reservoir
515-20 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→19.9 Å / Num. obs: 101836 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.076 / Net I/σ(I): 12.5
Reflection shellResolution: 1.95→1.98 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.35 / % possible all: 94
Reflection
*PLUS
Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.297

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER TECHNIQUES
Starting model: 1OAT

1oat


Resolution: 1.95→19.6 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 7077 7 %RANDOM
Rwork0.204 ---
obs0.206 101836 97 %-
Displacement parametersBiso mean: 25.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9483 0 75 744 10302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.021
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.95

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