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- PDB-7ta0: Human Ornithine Aminotransferase (hOAT) soaked with 5-aminovaleri... -

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Basic information

Entry
Database: PDB / ID: 7ta0
TitleHuman Ornithine Aminotransferase (hOAT) soaked with 5-aminovaleric acid
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Human Ornithine Aminotransferase / hOAT / OAT / PLP / 5-aminovaleric acid / soaking
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-I3B / PHOSPHATE ION / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsButrin, A. / Liu, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01CA260250-01 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Determination of the pH dependence, substrate specificity, and turnovers of alternative substrates for human ornithine aminotransferase.
Authors: Butrin, A. / Butrin, A. / Wawrzak, Z. / Moran, G.R. / Liu, D.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)147,0168
Polymers145,7813
Non-polymers1,2355
Water5,855325
1
A: Ornithine aminotransferase, mitochondrial
B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9795
Polymers97,1872
Non-polymers7923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-67 kcal/mol
Surface area25620 Å2
MethodPISA
2
C: Ornithine aminotransferase, mitochondrial
hetero molecules

C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0746
Polymers97,1872
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area10870 Å2
ΔGint-72 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.906, 114.906, 185.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11C-631-

HOH

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Components

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


Mass: 48593.668 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-I3B / 5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid


Mass: 348.289 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H21N2O7P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion ...Details: Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. 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 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 5-aminovaleric acid was added to the drop with crystals. The crystals were soaked for different time periods from 3 to 59 minutes. After soaking, crystals were transferred into a 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: 1.127 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.326→99.512 Å / Num. obs: 61264 / % possible obs: 99.9 % / Redundancy: 15.3 % / Biso Wilson estimate: 41.16 Å2 / CC1/2: 0.994 / Net I/σ(I): 7
Reflection shellResolution: 2.326→2.366 Å / Num. unique obs: 2995 / CC1/2: 0.33 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAT

1oat


Resolution: 2.33→99.51 Å / SU ML: 0.332 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.964
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.236 3097 5.07 %
Rwork0.214 --
obs0.215 61130 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.8 Å2
Refinement stepCycle: LAST / Resolution: 2.33→99.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9536 0 10 325 9871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029769
X-RAY DIFFRACTIONf_angle_d0.55413276
X-RAY DIFFRACTIONf_dihedral_angle_d7.5521353
X-RAY DIFFRACTIONf_chiral_restr0.0471467
X-RAY DIFFRACTIONf_plane_restr0.0041703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.40681290.36182555X-RAY DIFFRACTION98
2.36-2.40.35941250.34612575X-RAY DIFFRACTION99
2.4-2.440.35381470.33142603X-RAY DIFFRACTION100
2.44-2.490.30491310.30512602X-RAY DIFFRACTION100
2.49-2.540.37771210.29172657X-RAY DIFFRACTION100
2.54-2.590.30791580.29042562X-RAY DIFFRACTION100
2.59-2.640.31241500.28032621X-RAY DIFFRACTION100
2.64-2.70.2781490.2662598X-RAY DIFFRACTION100
2.7-2.770.29441300.26892644X-RAY DIFFRACTION100
2.77-2.850.33811360.26162646X-RAY DIFFRACTION100
2.85-2.930.29281380.25532623X-RAY DIFFRACTION100
2.93-3.030.28181390.24312671X-RAY DIFFRACTION100
3.03-3.130.26521380.24992587X-RAY DIFFRACTION99
3.13-3.260.27421380.22722605X-RAY DIFFRACTION99
3.26-3.410.24721620.2232602X-RAY DIFFRACTION100
3.41-3.590.27981610.21112646X-RAY DIFFRACTION100
3.59-3.810.21441400.18882642X-RAY DIFFRACTION100
3.81-4.110.18041500.17362680X-RAY DIFFRACTION100
4.11-4.520.17951350.16242671X-RAY DIFFRACTION100
4.52-5.170.15811420.16162683X-RAY DIFFRACTION100
5.17-6.520.23541300.19282712X-RAY DIFFRACTION99
6.52-99.510.15441480.15932848X-RAY DIFFRACTION99

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