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- PDB-5vwo: Ornithine aminotransferase inactivated by (1R,3S,4S)-3-amino-4-fl... -

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Basic information

Entry
Database: PDB / ID: 5vwo
TitleOrnithine aminotransferase inactivated by (1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP)
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Aminotransferase / Mechanism-based inactivator / PLP
Function / homology
Function and homology information


arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to 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) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, 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-9QJ / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.773 Å
AuthorsMascarenhas, R. / Liu, D. / Le, H. / Silverman, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01 DA030604 United States
CitationJournal: Biochemistry / Year: 2017
Title: Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover.
Authors: Mascarenhas, R. / Le, H.V. / Clevenger, K.D. / Lehrer, H.J. / Ringe, D. / Kelleher, N.L. / Silverman, R.B. / Liu, D.
History
DepositionMay 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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, mitochondrial
B: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,6566
Polymers134,5813
Non-polymers1,0753
Water23,5821309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-62 kcal/mol
Surface area42770 Å2
Unit cell
Length a, b, c (Å)115.305, 115.305, 187.991
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-808-

HOH

21C-752-

HOH

31C-1023-

HOH

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Components

#1: Protein Ornithine aminotransferase, mitochondrial / / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase


Mass: 44860.320 Da / Num. of mol.: 3 / Fragment: UNP residues 36-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical ChemComp-9QJ / (1S,3S,4E)-3-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-4-iminocyclopentane-1-carboxylic acid


Mass: 358.284 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H19N2O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1309 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: NaCl (175mM), 8-10% (v/v) PEG 6000

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.773→50 Å / Num. obs: 216569 / % possible obs: 99.8 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Χ2: 0.957 / Net I/σ(I): 8.6 / Num. measured all: 1315591
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.773-1.817.568650.5680.7930.82999
1.81-1.848.568690.6630.7160.83199.5
1.84-1.888.768510.7590.5780.84699.6
1.88-1.928.969090.7860.5180.85999.6
1.92-1.96969130.8550.4060.87499.6
1.96-29.268970.8760.310.88699.60.9220.974
2-2.059.369250.9160.2350.90399.80.7040.743
2.05-2.119.369560.9460.190.91599.80.5720.604
2.11-2.179.469240.9690.1420.92499.90.4250.449
2.17-2.249.469390.980.1180.89499.90.3540.373
2.24-2.329.469740.9860.090.8971000.2690.284
2.32-2.429.569790.990.0740.8881000.2220.234
2.42-2.539.669570.9930.0570.9161000.1710.181
2.53-2.669.869790.9950.0440.9411000.1320.139
2.66-2.8310.170300.9960.0340.9971000.1040.11
2.83-3.0410.470180.9970.0271.1151000.0830.088
3.04-3.3510.570280.9980.0231.2921000.0690.073
3.35-3.8310.270690.9980.0181.3971000.0560.059
3.83-4.831071460.9990.0131.0591000.040.042
4.83-509.873240.9980.0110.702990.0320.033

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAT
Resolution: 1.773→44.09 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 2017 1.48 %
Rwork0.178 --
obs0.178 216569 79.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.95 Å2
Refinement stepCycle: LAST / Resolution: 1.773→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9483 0 72 1309 10864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079905
X-RAY DIFFRACTIONf_angle_d1.11513499
X-RAY DIFFRACTIONf_dihedral_angle_d12.43712
X-RAY DIFFRACTIONf_chiral_restr0.0481493
X-RAY DIFFRACTIONf_plane_restr0.0051746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7732-1.79970.4158670.30794221X-RAY DIFFRACTION37
1.7997-1.82780.3232810.3045280X-RAY DIFFRACTION45
1.8278-1.85780.3047840.29795663X-RAY DIFFRACTION49
1.8578-1.88980.3093850.28665850X-RAY DIFFRACTION50
1.8898-1.92420.333920.28585999X-RAY DIFFRACTION52
1.9242-1.96120.3192910.27056276X-RAY DIFFRACTION54
1.9612-2.00120.31311020.24456675X-RAY DIFFRACTION57
2.0012-2.04470.29661000.22337167X-RAY DIFFRACTION62
2.0447-2.09230.29321220.22068023X-RAY DIFFRACTION69
2.0923-2.14460.26351430.20859396X-RAY DIFFRACTION81
2.1446-2.20260.24861660.212110459X-RAY DIFFRACTION91
2.2026-2.26740.25261570.211211276X-RAY DIFFRACTION96
2.2674-2.34060.26831730.206711425X-RAY DIFFRACTION98
2.3406-2.42420.20541720.203811492X-RAY DIFFRACTION99
2.4242-2.52130.25031710.197211595X-RAY DIFFRACTION100
2.5213-2.6360.25641790.194211559X-RAY DIFFRACTION100
2.636-2.7750.20791640.188711576X-RAY DIFFRACTION100
2.775-2.94880.22221750.182211597X-RAY DIFFRACTION100
2.9488-3.17640.21451720.177211564X-RAY DIFFRACTION100
3.1764-3.4960.19321720.16311583X-RAY DIFFRACTION100
3.496-4.00160.17311740.139211627X-RAY DIFFRACTION100
4.0016-5.04040.141780.120911582X-RAY DIFFRACTION100
5.0404-44.10760.13221760.130311488X-RAY DIFFRACTION99

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