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- PDB-7lk1: Ornithine Aminotransferase (OAT) with its potent inhibitor - (S)-... -

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Basic information

Entry
Database: PDB / ID: 7lk1
TitleOrnithine Aminotransferase (OAT) with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) - 1 Hour Soaking
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Ornithine Aminotransferase / OAT / aminotransferase / inhibitor / inactivator / SS-1-148 / soaking
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
Chem-Y37 / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 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
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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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)135,7106
Polymers134,5813
Non-polymers1,1293
Water13,799766
1
A: Ornithine aminotransferase, mitochondrial
hetero molecules

A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4734
Polymers89,7212
Non-polymers7532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area10420 Å2
ΔGint-62 kcal/mol
Surface area25670 Å2
MethodPISA
2
B: Ornithine aminotransferase, mitochondrial
hetero molecules

C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4734
Polymers89,7212
Non-polymers7532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-y-1,x-y-1,z-1/31
Buried area10380 Å2
ΔGint-59 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.650, 115.650, 186.690
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
11A-665-

HOH

21A-841-

HOH

31C-878-

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-Y37 / (1R,4R)-4-fluoro-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-2-ene-1-carboxylic acid


Mass: 376.274 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H18FN2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition ...Details: The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 10% PEG 6000, 200 mM NaCl, 10% glycerol, 100 mM Tricine pH 7.8. Once the holoenzyme crystals reached their maximum size, 2 uL of 16 mM SS-1-148 was added to the drop with crystals. The crystals were soaked for 1 h, transferred into cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.79→36.32 Å / Num. obs: 136181 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.028 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
1.79-1.849.82.4870.999790.3440.833100
8.01-36.3290.03541.816870.9990.01298.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1oat


Resolution: 1.79→36.32 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 6740 4.95 %
Rwork0.216 129365 -
obs0.2172 136105 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129 Å2 / Biso mean: 44.5205 Å2 / Biso min: 19.4 Å2
Refinement stepCycle: final / Resolution: 1.79→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9546 0 0 766 10312
Biso mean---46.54 -
Num. residues----1211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.79-1.810.42372200.383342704490
1.81-1.830.37232220.365142434465
1.83-1.850.36662080.342242754483
1.85-1.880.38071960.326543274523
1.88-1.90.35552630.324241954458
1.9-1.930.32342480.315743144562
1.93-1.960.30612220.30142364458
1.96-1.980.30612660.303342374503
1.98-2.020.35252130.297442434456
2.02-2.050.31412500.29142944544
2.05-2.080.3181940.297443084502
2.08-2.120.32071920.286642864478
2.12-2.160.29222400.27342574497
2.16-2.210.31212460.281542734519
2.21-2.260.28242150.274343144529
2.26-2.310.31182710.264842414512
2.31-2.370.30222340.264142994533
2.37-2.430.29152440.26542664510
2.43-2.50.29412510.25742694520
2.5-2.580.27912060.251643444550
2.58-2.670.2762180.242943054523
2.67-2.780.24541800.235643694549
2.78-2.910.24392100.229743304540
2.91-3.060.29111990.22143634562
3.06-3.250.23662080.217543524560
3.25-3.50.22742190.203143654584
3.5-3.850.21032410.183643714612
3.86-4.410.19122110.163743704581
4.41-5.550.1672430.156344274670
5.56-36.320.16552100.15746224832

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