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- PDB-6oia: (1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carbo... -

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Basic information

Entry
Database: PDB / ID: 6oia
Title(1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carboxylic acid hydrochloride, a potent inhibitor of ornithine aminotransferase
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Human Ornithine Aminotransferase (hOAT) Mechanism Based Inhibitors Hepatocellular Carcinoma 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) ...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-MQ4 / PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.777 Å
AuthorsCatlin, D.S. / Liu, D. / Moschitto, M.J. / Doubleday, P.F. / Kelleher, N. / Silverman, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Mechanism of Inactivation of Ornithine Aminotransferase by (1S,3S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)cyclopentane-1-carboxylic Acid.
Authors: Moschitto, M.J. / Doubleday, P.F. / Catlin, D.S. / Kelleher, N.L. / Liu, D. / Silverman, R.B.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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)135,98110
Polymers134,5813
Non-polymers1,4007
Water19,4381079
1
A: Ornithine aminotransferase, mitochondrial
B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6367
Polymers89,7212
Non-polymers9165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-66 kcal/mol
Surface area25960 Å2
MethodPISA
2
C: Ornithine aminotransferase, mitochondrial
hetero molecules

C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6896
Polymers89,7212
Non-polymers9694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area11880 Å2
ΔGint-66 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.824, 115.824, 187.644
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-726-

HOH

21C-941-

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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MQ4 / (1S)-3-amino-4-[(2S)-1,1,1-trifluoro-3-oxopropan-2-yl]cyclopent-3-ene-1-carboxylic acid


Mass: 237.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10F3NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1079 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 6000, 200 mM NaCl, 2.5 % Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 125931 / % possible obs: 89.78 % / Redundancy: 10.9 % / Biso Wilson estimate: 19.52 Å2 / Net I/σ(I): 1.37
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 7324

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.777→29.487 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.93
RfactorNum. reflection% reflection
Rfree0.1891 6318 5.02 %
Rwork0.1614 --
obs0.1628 125923 89.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.89 Å2 / Biso mean: 29.082 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 1.777→29.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9483 0 89 1079 10651
Biso mean--33.65 37.91 -
Num. residues----1212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079943
X-RAY DIFFRACTIONf_angle_d0.8613535
X-RAY DIFFRACTIONf_chiral_restr0.0581494
X-RAY DIFFRACTIONf_plane_restr0.0051748
X-RAY DIFFRACTIONf_dihedral_angle_d4.0148166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7769-1.79710.3098800.27151699177939
1.7971-1.81820.3581390.28222500263957
1.8182-1.84040.26251660.26113017318368
1.8404-1.86370.27971690.23833305347476
1.8637-1.88820.26081670.22833480364780
1.8882-1.91410.25142020.223650385283
1.9141-1.94140.25221790.21533765394485
1.9414-1.97040.26152410.20663901414289
1.9704-2.00120.25572510.20264094434594
2.0012-2.0340.21962210.19714294451597
2.034-2.06910.23532130.19754341455498
2.0691-2.10670.21072100.19394330454098
2.1067-2.14720.20572360.18654287452398
2.1472-2.1910.21472230.17874343456698
2.191-2.23860.21691930.1684307450098
2.2386-2.29070.19822330.16374329456298
2.2907-2.34790.20062500.16384331458198
2.3479-2.41140.18372020.16654320452297
2.4114-2.48230.20382410.17074270451197
2.4823-2.56240.19952670.16574267453497
2.5624-2.65390.22012300.16674269449997
2.6539-2.76010.19942530.16254307456096
2.7601-2.88560.1762110.15914265447696
2.8856-3.03760.17092030.15534327453096
3.0376-3.22770.16221990.15974283448296
3.2277-3.47660.19372420.14894249449195
3.4766-3.82570.16012300.13344248447895
3.8257-4.37780.15142180.1224280449894
4.3778-5.50970.14992140.12224256447093
5.5097-29.4910.13442350.14344291452691
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7681-0.26580.52310.602-0.9061.37080.00960.1368-0.0191-0.0922-0.0065-0.21380.06320.2333-0.00760.29690.03680.09490.43390.04980.331680.3475-24.3579-66.4076
20.95970.24450.07610.53160.18310.44410.04440.0320.0292-0.0630.0078-0.12040.03570.1559-0.01670.26980.20630.01640.37580.00760.207382.6938-38.0543-52.188
30.2848-0.0265-0.15040.28290.03340.41270.018-0.1697-0.04050.03850.0297-0.01180.20740.33230.030.26920.1066-0.02060.1370.0390.0562.0113-28.1679-38.2788
40.7587-0.0116-0.26670.46190.00151.17410.07720.04850.2231-0.02170.0573-0.2262-0.15540.2305-0.04440.19320.0477-0.00680.64570.0080.382390.4476-22.6468-42.1542
50.39980.69150.2061.63210.15521.2214-0.0014-0.0523-0.15430.0025-0.0069-0.02690.170.0407-0.02620.36520.04180.01510.10340.0830.183850.981-48.6778-41.5683
60.49830.12830.00240.5819-0.04370.05780.0391-0.007-0.09140.03860.01480.02610.09470.03870.01510.42470.1376-0.01530.0830.01880.180958.1162-50.6187-60.0609
70.301-0.07340.10980.1958-0.03610.53040.00310.07870.0238-0.0784-0.0445-0.05740.07230.22410.0330.23370.03680.00650.08990.03530.099356.7632-21.6754-60.2977
80.194-0.16370.0780.69070.05320.11660.01490.0740.0044-0.1018-0.05990.02950.07140.053-0.02560.31570.073-0.02430.04840.03180.064949.933-25.4451-70.135
90.74870.24320.25920.73820.11030.50440.01140.0284-0.0385-0.04660.00260.07650.20770.0749-0.00820.29780.06670.0210.11510.01370.120352.2099-37.3624-66.2316
101.15130.1022-0.40730.5331-0.29841.1790.0608-0.0598-0.05070.06550.03980.11470.0847-0.1199-0.02130.40560.0005-0.00440.11070.03470.234940.8673-50.5924-61.6984
110.780.9535-0.1841.1989-0.05640.9078-0.07620.08870.0108-0.14820.05580.16460.0604-0.17850.04150.3256-0.1344-0.1950.22330.07810.37037.8703-12.4062-81.6539
120.07640.09150.01250.4157-0.00610.05910.02340.04410.0015-0.03960.08390.1370.042-0.12480.00230.2191-0.163-0.08460.31790.23150.5219-1.6312-14.1366-64.124
130.07890.0523-0.03380.1807-0.10570.18180.0583-0.0507-0.0060.07220.10470.2863-0.0406-0.17440.02960.17630.00610.0604-0.10010.12780.22723.199-3.6274-53.259
140.40240.40670.09280.70590.10370.20210.0157-0.0299-0.084-0.00970.03180.07220.0859-0.0524-0.01790.2108-0.02210.04390.02630.06260.199627.0864-15.0935-47.1632
150.0770.06460.11720.3258-0.11510.37130.0554-0.04950.03070.07470.10860.21710.0117-0.2237-0.07530.1550.00460.07960.15510.13380.383911.5792-6.1921-49.2909
160.20330.2822-0.04090.71940.08230.36020.0520.0442-0.0738-0.10550.10540.01620.1415-0.08470.06030.4205-0.2512-0.15390.16590.14270.52079.0354-30.5103-63.1201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 61 )A36 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 105 )A62 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 344 )A106 - 344
4X-RAY DIFFRACTION4chain 'A' and (resid 345 through 439 )A345 - 439
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 61 )B36 - 61
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 105 )B62 - 105
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 220 )B106 - 220
8X-RAY DIFFRACTION8chain 'B' and (resid 221 through 295 )B221 - 295
9X-RAY DIFFRACTION9chain 'B' and (resid 296 through 389 )B296 - 389
10X-RAY DIFFRACTION10chain 'B' and (resid 390 through 439 )B390 - 439
11X-RAY DIFFRACTION11chain 'C' and (resid 36 through 61 )C36 - 61
12X-RAY DIFFRACTION12chain 'C' and (resid 62 through 105 )C62 - 105
13X-RAY DIFFRACTION13chain 'C' and (resid 106 through 220 )C106 - 220
14X-RAY DIFFRACTION14chain 'C' and (resid 221 through 263 )C221 - 263
15X-RAY DIFFRACTION15chain 'C' and (resid 264 through 344 )C264 - 344
16X-RAY DIFFRACTION16chain 'C' and (resid 345 through 439 )C345 - 439

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