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- PDB-6v8d: Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohex... -

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Basic information

Entry
Database: PDB / ID: 6v8d
TitleDesign, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Human Ornithine Aminotransferase (hOAT) / Mechanism Based Inactivator / PLP Hepatocellular Carcinoma (HCC)
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
(3Z)-3-iminocyclohex-1-ene-1-carboxylic acid / PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZhu, W. / Doubleday, P.T. / Catlin, D.S. / Weerawarna, P. / Butrin, A. / Shen, S. / Kelleher, N.L. / Liu, D. / Silverman, R.B.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA030604
CitationJournal: To Be Published
Title: Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators
Authors: Zhu, W. / Doubleday, P.T. / Catlin, D.S. / Weerawarna, P. / Butrin, A. / Shen, S. / Kelleher, N.L. / Liu, D. / Silverman, R.B.
History
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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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)135,7409
Polymers134,5813
Non-polymers1,1596
Water9,854547
1
A: Ornithine aminotransferase, mitochondrial
B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4936
Polymers89,7212
Non-polymers7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-67 kcal/mol
Surface area25350 Å2
MethodPISA
2
C: Ornithine aminotransferase, mitochondrial
hetero molecules

C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4936
Polymers89,7212
Non-polymers7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11560 Å2
ΔGint-55 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.596, 111.958, 57.873
Angle α, β, γ (deg.)90.000, 104.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-769-

HOH

21C-686-

HOH

31C-724-

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
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O78 / (3Z)-3-iminocyclohex-1-ene-1-carboxylic acid


Mass: 139.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 16.5% PEG 1000 240 mM NaCl 25% glycerol 50 mM Tricine pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→32 Å / Num. obs: 54461 / % possible obs: 91.73 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 15
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 3671 / CC1/2: 0.891

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAT

1oat


Resolution: 2.25→31.36 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 2703 4.96 %
Rwork0.1568 51758 -
obs0.1587 54461 91.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.04 Å2 / Biso mean: 29.9815 Å2 / Biso min: 14.92 Å2
Refinement stepCycle: final / Resolution: 2.25→31.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9450 0 75 547 10072
Biso mean--30.89 35.86 -
Num. residues----1206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.290.265990.17661710180958
2.29-2.340.25471070.16661981208866
2.34-2.380.22661230.1662194231775
2.38-2.430.20591440.16732596274088
2.43-2.490.21291350.1652825296096
2.49-2.550.2191370.16572913305098
2.55-2.620.23241530.1582948310199
2.62-2.70.18911540.1582889304399
2.7-2.790.19811540.15462934308899
2.79-2.890.24011400.16052957309799
2.89-30.19371450.16062889303499
3-3.140.18831680.15452907307598
3.14-3.30.19721720.1542877304998
3.3-3.510.1591510.15052624277588
3.51-3.780.16961440.14722907305198
3.78-4.160.17271710.14292952312399
4.16-4.760.20661370.14472936307398
4.76-5.990.21181290.17462949307897
5.99-31.360.17961400.16622770291091

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