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- PDB-7lk0: Ornithine Aminotransferase (OAT) cocrystallized with its potent i... -

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Basic information

Entry
Database: PDB / ID: 7lk0
TitleOrnithine Aminotransferase (OAT) cocrystallized with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148)
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Ornithine Aminotransferase / OAT / aminotransferase / inhibitor / inactivator / SS-1-148
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-Y3D / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsButrin, A. / Shen, S. / Liu, D. / Silverman, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Turnover and Inactivation Mechanisms for ( S )-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase.
Authors: Shen, S. / Butrin, A. / Doubleday, P.F. / Melani, R.D. / Beaupre, B.A. / Tavares, M.T. / Ferreira, G.M. / Kelleher, N.L. / Moran, G.R. / Liu, D. / Silverman, R.B.
History
DepositionFeb 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: 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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)135,6986
Polymers134,5813
Non-polymers1,1173
Water10,485582
1
A: Ornithine aminotransferase, mitochondrial
hetero molecules

A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4654
Polymers89,7212
Non-polymers7452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-1/31
Buried area10370 Å2
ΔGint-57 kcal/mol
Surface area25340 Å2
MethodPISA
2
B: Ornithine aminotransferase, mitochondrial
hetero molecules

B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4654
Polymers89,7212
Non-polymers7452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area10380 Å2
ΔGint-63 kcal/mol
Surface area25390 Å2
MethodPISA
3
C: Ornithine aminotransferase, mitochondrial
hetero molecules

C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4654
Polymers89,7212
Non-polymers7452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+y,y,-z-2/31
Buried area10350 Å2
ΔGint-62 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.707, 192.707, 56.804
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-627-

HOH

21A-642-

HOH

31B-675-

HOH

41C-647-

HOH

51C-664-

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-Y3D / (1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-1-carboxylic acid


Mass: 372.267 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H17N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: OAT was buffer exchanged into crystallization buffer (50 mM Tricine pH 7.8) supplied with 1 mM 2-ketoglutarate. Then the protein was concentrated to 6 mg/mL. For each hanging drop, 2 uL of ...Details: OAT was buffer exchanged into crystallization buffer (50 mM Tricine pH 7.8) supplied with 1 mM 2-ketoglutarate. Then the protein was concentrated to 6 mg/mL. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of 10 mM SS-1-148. The crystals with the best morphology and size grew in a final condition containing 10% PEG 6000, 200 mM NaCl, 10% glycerol, 100 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: 1.1271 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.955→48.18 Å / Num. obs: 79187 / % possible obs: 91.6 % / Redundancy: 8.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.083 / Net I/σ(I): 5.6
Reflection shellResolution: 1.955→1.989 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3113 / CC1/2: 0.783 / Rpim(I) all: 0.604 / % possible all: 72.1

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAT

1oat


Resolution: 1.96→48.18 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 3853 4.91 %
Rwork0.247 74630 -
obs0.248 78483 90.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.25 Å2 / Biso mean: 36.934 Å2 / Biso min: 6.99 Å2
Refinement stepCycle: final / Resolution: 1.96→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9432 0 75 582 10089
Biso mean--30.36 33.12 -
Num. residues----1207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-1.980.3511090.32092006211568
1.98-20.3509990.28332334243380
2-2.030.291240.29442345246979
2.03-2.060.2952920.28752393248582
2.06-2.090.289970.27532420251782
2.09-2.120.31161280.27762360248880
2.12-2.150.31741410.26542217235877
2.15-2.190.30081280.26192470259884
2.19-2.220.28321310.24752528265988
2.22-2.270.2761430.26332574271787
2.27-2.310.29771340.24572654278891
2.31-2.360.27871170.24872698281591
2.36-2.410.3121300.252734286493
2.41-2.460.29181460.23742771291794
2.46-2.520.27291400.22672799293996
2.52-2.590.2581480.22432787293595
2.59-2.670.27011590.23652874303398
2.67-2.760.26761480.23572874302298
2.76-2.850.26871510.23442888303999
2.85-2.970.27511630.240729053068100
2.97-3.10.27111480.24442919306799
3.1-3.270.26171320.24182935306799
3.27-3.470.24661960.23682860305699
3.47-3.740.22871340.2322935306999
3.74-4.120.23161670.22092862302998
4.12-4.710.2531470.2292888303597
4.71-5.930.25751460.25922912305898
5.94-48.180.26731550.27932688284389
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)
10.52690.128-0.29650.7057-0.08310.1595-0.06570.13080.0131-0.1560.21510.4165-0.0375-0.36470.1181-0.02580.0271-0.0060.3440.19570.438850.8826-46.4853-12.7434
20.32480.0392-0.25611.5624-0.50440.89170.1227-0.05290.16270.1708-0.0852-0.1823-0.1027-0.0189-0.01040.1011-0.0060.03280.15460.05110.012776.374-45.14910.7559
30.81760.0197-0.28960.8254-0.26050.68140.0038-0.08-0.02240.3098-0.0040.1037-0.1321-0.0319-0.04840.17340.0010.01190.13760.05610.056870.3664-51.619.141
41.50310.3234-0.00211.0246-0.75941.09640.0554-0.0815-0.21150.09150.13310.22150.008-0.2721-0.08750.08760.03910.05940.19860.04460.234959.7222-49.66222.3872
50.6672-0.3421-0.39560.8004-0.17372.14510.0179-0.0045-0.2845-0.09210.19750.31840.34-0.36040.09610.0713-0.0676-0.02040.33150.11680.445348.1061-61.1528-4.8107
60.7041-0.5391-0.20421.66370.27261.55950.30850.04060.6122-0.4039-0.1429-0.0147-0.36190.3336-0.20640.4452-0.01140.21130.52040.0160.657627.1919-73.5953-7.9459
70.48680.0773-0.41080.90390.07560.80990.07120.04810.25020.25490.0817-0.34070.0262-0.0093-0.15960.3178-0.09440.00570.49-0.09030.687537.1828-92.51339.9999
80.5335-0.5321-0.05530.53690.17520.67810.01220.09030.00460.02410.06340.4650.1204-0.1158-0.03890.3673-0.04230.08240.4145-0.01130.68310.4765-99.49168.8346
91.0667-0.0472-0.23851.4456-0.30420.6982-0.28410.0078-0.09360.00190.1145-0.17910.3133-0.23770.17620.4793-0.02330.1160.3691-0.00420.665111.3277-93.296119.0934
100.64590.1665-0.84161.3761-0.01151.11290.0822-0.00020.2580.08680.15030.0372-0.1518-0.0902-0.21680.3713-0.08290.07240.4624-0.06360.686423.4464-83.761913.533
111.0361-0.05340.34911.1376-0.09992.30590.3402-0.0613-0.08860.12130.0760.3762-0.4501-0.4849-0.41660.4827-0.05360.29190.5882-0.01190.978119.3768-66.70794.7133
121.5859-0.01040.1531.0585-0.21521.32790.27540.0552-0.47530.0316-0.0981-0.04160.47480.2025-0.15420.44950.0391-0.14530.5122-0.02570.52047.1758-41.9018-16.8051
132.00310.10790.35690.69350.21340.9260.0824-0.02830.36270.011-0.0968-0.18-0.0088-0.24660.02340.26230.02540.00630.3911-0.020.49374.8612-14.9254-9.9703
141.121-0.35920.31431.9809-0.19960.99520.1003-0.4094-0.06350.0379-0.13860.0459-0.08760.12840.06760.2702-0.0280.00830.5198-0.03920.45319.9175-18.79380.1483
151.377-0.14640.92031.79530.57871.78590.24180.02660.0280.1085-0.101-0.24860.33360.1513-0.12190.3540.0136-0.06070.43510.03790.469212.1096-34.0364-5.4421
161.75310.6468-1.02610.46140.04471.41720.21440.1530.25760.05190.12490.07210.2210.3116-0.31930.44780.1794-0.13760.6529-0.00430.693628.9521-39.014-14.327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 106 )A38 - 106
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 220 )A107 - 220
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 295 )A221 - 295
4X-RAY DIFFRACTION4chain 'A' and (resid 296 through 389 )A296 - 389
5X-RAY DIFFRACTION5chain 'A' and (resid 390 through 439 )A390 - 439
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 82 )B38 - 82
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 141 )B83 - 141
8X-RAY DIFFRACTION8chain 'B' and (resid 142 through 220 )B142 - 220
9X-RAY DIFFRACTION9chain 'B' and (resid 221 through 263 )B221 - 263
10X-RAY DIFFRACTION10chain 'B' and (resid 264 through 389 )B264 - 389
11X-RAY DIFFRACTION11chain 'B' and (resid 390 through 439 )B390 - 439
12X-RAY DIFFRACTION12chain 'C' and (resid 37 through 141 )C37 - 141
13X-RAY DIFFRACTION13chain 'C' and (resid 142 through 220 )C142 - 220
14X-RAY DIFFRACTION14chain 'C' and (resid 221 through 263 )C221 - 263
15X-RAY DIFFRACTION15chain 'C' and (resid 264 through 389 )C264 - 389
16X-RAY DIFFRACTION16chain 'C' and (resid 390 through 439 )C390 - 439

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