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- PDB-7t9z: Human Ornithine Aminotransferase (hOAT) crystallized at pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 7t9z
TitleHuman Ornithine Aminotransferase (hOAT) crystallized at pH 6.0
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Human Ornithine Aminotransferase / hOAT / OAT / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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

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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)146,5226
Polymers145,7813
Non-polymers7413
Water10,377576
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A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8412
Polymers48,5941
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8412
Polymers48,5941
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8412
Polymers48,5941
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.910, 110.860, 56.930
Angle α, β, γ (deg.)90.000, 106.404, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

21A-665-

HOH

31B-647-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 38 through 44 or resid 47...
d_2ens_1(chain "B" and (resid 38 through 44 or resid 47...
d_3ens_1(chain "C" and (resid 38 through 44 or resid 47...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROPHEA1 - 7
d_12ens_1GLUTYRA10 - 11
d_13ens_1TYRGLUA13 - 26
d_14ens_1GLYASPA28 - 69
d_15ens_1LEUPHEA71 - 94
d_16ens_1TYRGLYA96 - 142
d_17ens_1THRALAA144 - 309
d_18ens_1ASNASPA311 - 313
d_19ens_1LEUTHRA315 - 348
d_110ens_1ASPTRPA350 - 354
d_111ens_1VALALAA356 - 367
d_112ens_1PROTHRA369 - 370
d_113ens_1GLYILEA372 - 383
d_114ens_1GLUASNA385 - 396
d_115ens_1THRPHEA398 - 402
d_116ens_1PLPPLPB
d_21ens_1PROPHEC1 - 7
d_22ens_1GLUTYRC10 - 11
d_23ens_1TYRGLUC13 - 26
d_24ens_1GLYASPC28 - 69
d_25ens_1LEUPHEC71 - 94
d_26ens_1TYRGLYC96 - 142
d_27ens_1THRALAC144 - 309
d_28ens_1ASNASPC311 - 313
d_29ens_1LEUTHRC315 - 348
d_210ens_1ASPTRPC350 - 354
d_211ens_1VALALAC356 - 367
d_212ens_1PROTHRC369 - 370
d_213ens_1GLYILEC372 - 383
d_214ens_1GLUASNC385 - 396
d_215ens_1THRPHEC398 - 402
d_216ens_1PLPPLPD
d_31ens_1PROPHEE1 - 7
d_32ens_1GLUTYRE10 - 11
d_33ens_1TYRGLUE13 - 26
d_34ens_1GLYASPE28 - 69
d_35ens_1LEUPHEE71 - 94
d_36ens_1TYRGLYE96 - 142
d_37ens_1THRALAE144 - 309
d_38ens_1ASNASPE311 - 313
d_39ens_1LEUTHRE315 - 348
d_310ens_1ASPTRPE350 - 354
d_311ens_1VALALAE356 - 367
d_312ens_1PROTHRE369 - 370
d_313ens_1GLYILEE372 - 383
d_314ens_1GLUASNE385 - 396
d_315ens_1THRPHEE398 - 402
d_316ens_1PLPPLPF

NCS oper:
IDCodeMatrixVector
1given(0.37818394109, -0.83126294656, 0.407404983252), (-0.832004581342, -0.498167950402, -0.244125110995), (0.405888264585, -0.246638615932, -0.880013698645)23.6185193341, 52.3174750167, 26.7571636424
2given(-0.378343412943, -0.830358012627, -0.409098805606), (0.832687590933, -0.498346046234, 0.241417882746), (-0.404336045622, -0.24931263319, 0.879974757105)23.6290794851, 52.3103571762, 26.8370567152

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


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Purified holo-hOAT was buffer-exchanged into 100 mM MES, 200 mM NaCl, 100 uM PLP, pH 6.0 buffer, and then concentrated to ~6 mg/mL. The crystallization was performed via the hanging drop ...Details: Purified holo-hOAT was buffer-exchanged into 100 mM MES, 200 mM NaCl, 100 uM PLP, pH 6.0 buffer, and then concentrated to ~6 mg/mL. The crystallization was performed via the hanging drop vapor diffusion method according to previously published conditions with 50 mM Tricine pH 7.8 substituted to 50 mM MES pH 6.0 buffer. The crystals grew at room temperature within three days and reached their maximum size in a week.

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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: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.99→96.1 Å / Num. obs: 60876 / % possible obs: 92.5 % / Redundancy: 3.4 % / CC1/2: 0.986 / Rpim(I) all: 0.133 / Net I/σ(I): 4.9
Reflection shellResolution: 1.99→2.02 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 14325 / CC1/2: 0.371

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAT
Resolution: 2.15→54.61 Å / Cross valid method: FREE R-VALUE / σ(F): 56.84 / Phase error: 31.097
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2759 3272 2.9 %
Rwork0.2656 109445 -
obs0.2706 112717 87.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.88 Å2
Refinement stepCycle: LAST / Resolution: 2.15→54.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9450 0 45 576 10071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00639723
X-RAY DIFFRACTIONf_angle_d0.664913210
X-RAY DIFFRACTIONf_chiral_restr0.04711462
X-RAY DIFFRACTIONf_plane_restr0.00511697
X-RAY DIFFRACTIONf_dihedral_angle_d5.52291329
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.535629373591
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.558752351079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.3161440.30535417X-RAY DIFFRACTION83.8
2.19-2.230.25941460.29855425X-RAY DIFFRACTION85.12
2.23-2.270.30541550.29755462X-RAY DIFFRACTION85.08
2.27-2.320.28791520.29075414X-RAY DIFFRACTION85.11
2.32-2.370.33911580.30435434X-RAY DIFFRACTION84.12
2.37-2.420.31481420.31095499X-RAY DIFFRACTION86.53
2.42-2.480.30671540.29725626X-RAY DIFFRACTION86.57
2.48-2.550.27971310.28875297X-RAY DIFFRACTION82.97
2.55-2.620.30661280.29474265X-RAY DIFFRACTION67.24
2.62-2.710.27131350.26624996X-RAY DIFFRACTION77.11
2.71-2.810.29311560.27975788X-RAY DIFFRACTION90.91
2.81-2.920.30581640.27255911X-RAY DIFFRACTION91.84
2.92-3.050.25611560.26425880X-RAY DIFFRACTION91.75
3.05-3.210.26181510.26095796X-RAY DIFFRACTION91.02
3.21-3.410.28921570.25525787X-RAY DIFFRACTION90.03
3.41-3.680.23651570.25045702X-RAY DIFFRACTION88.76
3.68-4.050.24371590.24295741X-RAY DIFFRACTION89.49
4.05-4.630.27041410.23825360X-RAY DIFFRACTION83.7
4.63-5.830.28851270.25314817X-RAY DIFFRACTION75.04
5.83-54.610.33541680.29786119X-RAY DIFFRACTION95.58
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.00365380483133-0.003430635137340.002550528830370.00395239194078-0.004366233253350.003402760880060.01188041404260.0132773001432-0.00824643782557-0.00324397231522-0.0072724340043-0.007622750546120.02366872208880.00702444019153-0.006295365652140.104016418110.0508548206663-0.04761430853850.1946710348370.02091755566290.043165497669515.6381437217-8.957680304220.716661166232
2-0.001000947724830.004472979199010.0031799291111-0.002193483457330.001177533727090.009628580262140.00195700994501-0.0196699021269-0.006198972132910.0109823712618-0.002799060392110.02042445653780.0190076992071-0.00758256499156-0.004522675314740.0521614361124-0.0318962691007-0.04631555880880.169461645969-0.0114694131452-0.110043207651-2.05740070112.04210726639.81752601672
30.0005059487213690.0003932729581040.00384129198353-0.00310153056930.002647913448690.00662484417290.00522582952497-0.0360177375105-0.009342950066020.0258539016871-0.0109597976996-0.02760325265440.01272695514150.0125037753623-0.03392404835540.07072274310890.00472031041482-0.08973124763190.2170733960770.0170827430212-0.1122675443926.956764514594.7124214860817.6113244281
40.001250840242110.0007265152144960.002156355371020.0006762097262750.001649053109980.004197030393790.007592739006640.00169548642643-0.00903556888996-0.0002866817177650.00785519607575-0.002435190443130.009741795185040.006633316591890.009470913882430.087468079310.0669628418297-0.04689810092950.177329977602-0.01008705484370.04856508350426.6333335931-4.2023549026212.4395244339
50.001919753356050.004216676981550.004919877247160.004234231368750.004952767462810.00577160987217-0.00971579586829-0.01073516632450.004284895791980.01649371016110.0236342432944-0.01136365394290.004514077011790.01036640604240.01514762091550.06871262159280.0381696683805-0.03341277120070.164256066298-0.02381833030720.027612548641437.320606542343.590629837934.6553891298
6-0.003164659020120.0002141697350090.00141320861755-0.0004234950245110.0005020239991190.006802813507650.002723719248770.01582626672520.0129528037345-0.02114172888520.001107759463240.00430790772799-0.0087581357350.01034206099250.004933217915480.0526028951899-0.0128789906011-0.0105159897820.159965588545-0.0166500924368-0.1045981522516.840831892945.601684539714.3130921183
70.00158560781765-0.000838121860754-0.0009395091992871.74486858957E-50.001163498188160.00282405132476-0.00447617993499-0.00292650103518-0.00246390261298-0.00352648506412-0.008965528437240.0019303355478-0.00261613896296-0.00753488989177-0.02012157028210.08184391442930.0233311977865-0.0283876976030.169589856057-0.00739585071484-0.017105483891820.401738036535.6693020795.85805457889
80.000725852949588-0.00246301979756-0.002497775320590.00250559048590.001020185085660.004840196832420.008894909815510.000541701854613-0.00296264575613-0.008244801082310.00895727358-0.0132802606295-0.002435917794750.01906992473460.02433444697560.0411238620814-0.001422907895140.003958650657730.169488613913-0.0321588856048-0.047956182603531.573047357246.899132816213.2859439446
90.002649157680420.002004016884760.001068511737510.00216111426509-7.65474367602E-50.001603781934810.008649476514290.00140386783518-0.01164466713670.004055807839220.00313900703091-0.002311161854750.00650924667030.000333068009178-0.0004997648730380.1345733554640.0304147361558-0.01864183112980.172770920329-0.03384808354480.093204062387636.416531364821.136529643822.9312202361
104.9113302371E-5-2.59230928862E-5-0.001231154780290.0005560097382070.002764152592830.009648276087850.000586108748468-0.004575185281490.0008225578169850.006108338120520.00107563677993-0.003133298676860.0120509340150.001953981892240.001442737623710.1023510590590.0480145926949-0.0379294616040.213463444248-0.03944493978860.049469217813342.211193987429.250163768127.5914341431
11-0.0001078905501070.000200397069082-4.2357568205E-5-4.42141407452E-5-6.52973356347E-54.16665135296E-50.00464100492451-0.0006482966309860.00360063713376-0.002507921483620.00172759492083-0.00177568168615-0.00167493388823-0.003749811751540.002809380743550.118538738295-0.003157962642830.02131146620850.1305138059630.01898203519570.042565606450521.554108619968.670520693311.0088185567
120.00209674331214-0.000905057564967-0.0005759180847010.00588610871577-0.01085599440950.02106169290220.0173661607518-0.005685041103710.0133470552808-0.003617603210220.0209693388385-0.00234348278818-0.003054220070360.02189990125550.02931943059920.117143675826-0.04059500594580.004937216387520.177417618822-0.01965268247040.081025483601226.688257722770.745195341330.3486793973
130.00620772590356-0.000595877309888-0.00400948484537-0.000416622611452-0.003470237982420.00894884801578-0.000261578937592-0.0156369463582-0.008445147333330.01599917785520.015835993871-0.000937542150730.00605326807544-0.01081523819390.02982389788120.0618611410210.0103002111973-0.02079311667070.212175855949-0.0226264099603-0.055424960198316.088377733545.330179024136.1275733549
140.00149295050858-0.002161015799590.002640751763370.00184769325549-0.001180994473070.004153507982880.00666370069026-0.00581852310967-0.003201226109960.004874800270910.003422446521530.006899068255950.000192243823688-0.00766347686230.02329761318560.0392413485820.0120534826706-0.002654836381970.137315780325-0.00433247634128-7.40961253828E-5-1.6380077753350.729304071627.0733753798
150.001778511463930.00205229651196-0.006837506001080.00329781784522-0.00443718287260.0169126760754-0.0111124382701-0.00444025910784-0.0009815667239810.006831728691820.00476290915130.002340527225920.00623553100226-0.00547870694729-0.01278697449930.07380529395530.02362435207730.03065332580920.128625547214-0.002057555201270.003864407344420.020019655772452.867098258439.7406281468
166.15490670105E-5-0.0002538302183520.00296975875880.001721091347710.0008243068540110.006498241965490.00631686305808-0.00786694641459-0.00124013699750.000891033980259-0.001503232096970.000824095668910.007107413088060.005801523289640.00358612072280.0551030223324-0.00585013270938-0.01011012941780.166840060757-0.0194818283343-0.026903943177615.633310046352.141083547539.4811748167
170.009158293207770.0083260010127-0.00778466911340.0204370137412-0.01610709379260.01424844869990.01621829458890.001437363509550.02357936750790.009146109448010.0264240919166-0.00322782540489-0.000885341943227-0.004639303444490.06681210388890.09486624648220.00461327252271-0.009813619976280.156167598844-0.05186142175180.040155833849910.959296774172.591985179236.2634178682
180.002015698185920.002938840646180.001579458344940.00483486829430.002069982251810.001058913084530.008859866946460.01308244839460.0151276652033-0.0003734222097130.009592949238160.00442368038562-0.00573318245428-0.001966376055110.0002773732489030.125556788156-0.008918949976680.03481563303050.183558523606-0.01847429966110.10506733577111.996094105979.502726487228.1857697329
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 38 through 105 )AA38 - 1051 - 68
22chain 'A' and (resid 106 through 220 )AA106 - 22069 - 183
33chain 'A' and (resid 221 through 389 )AA221 - 389184 - 352
44chain 'A' and (resid 390 through 439 )AA390 - 439353 - 402
55chain 'B' and (resid 38 through 105 )BC38 - 1051 - 68
66chain 'B' and (resid 106 through 220 )BC106 - 22069 - 183
77chain 'B' and (resid 221 through 263 )BC221 - 263184 - 226
88chain 'B' and (resid 264 through 362 )BC264 - 362227 - 325
99chain 'B' and (resid 363 through 389 )BC363 - 389326 - 352
1010chain 'B' and (resid 390 through 439 )BC390 - 439353 - 402
1111chain 'C' and (resid 38 through 61 )CE38 - 611 - 24
1212chain 'C' and (resid 62 through 105 )CE62 - 10525 - 68
1313chain 'C' and (resid 106 through 181 )CE106 - 18169 - 144
1414chain 'C' and (resid 182 through 220 )CE182 - 220145 - 183
1515chain 'C' and (resid 221 through 263 )CE221 - 263184 - 226
1616chain 'C' and (resid 264 through 326 )CE264 - 326227 - 289
1717chain 'C' and (resid 327 through 389 )CE327 - 389290 - 352
1818chain 'C' and (resid 390 through 439 )CE390 - 439353 - 402

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