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- PDB-3ruy: Crystal Structure of the Ornithine-oxo acid transaminase RocD fro... -

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Basic information

Entry
Database: PDB / ID: 3ruy
TitleCrystal Structure of the Ornithine-oxo acid transaminase RocD from Bacillus anthracis
ComponentsOrnithine aminotransferase
KeywordsTRANSFERASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / alpha and beta protein / PLP-dependent
Function / homology
Function and homology information


ornithine aminotransferase activity / ornithine aminotransferase / L-proline biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase, bacterial type / 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 ...Ornithine aminotransferase, bacterial type / 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
Ornithine aminotransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Brunzelle, J.S. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the Ornithine-oxo acid transaminase RocD from Bacillus anthracis
Authors: Anderson, S.M. / Wawrzak, Z. / Brunzelle, J.S. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine aminotransferase
B: Ornithine aminotransferase


Theoretical massNumber of molelcules
Total (without water)86,1442
Polymers86,1442
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-60 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.120, 98.291, 126.783
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ornithine aminotransferase / OAT / Ornithine-oxo-acid aminotransferase


Mass: 43072.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: rocD, BA_1154, GBAA_1154, BAS1071 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81TV3, ornithine aminotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailspyridoxal-5-phosphate covalently bound to lysine 255

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 12.5mM suberic acid, 12.5mM sebacic acid, 12.5mM hexadecanedioic acid, 12.5mM dodecanedioic acid, 40% ethanol, 100mM HEPES, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2011 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionHighest resolution: 2.65 Å / Num. all: 26350 / Num. obs: 25718 / % possible obs: 97.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.1 / Redundancy: 5.8 % / Biso Wilson estimate: 67.9 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2598 / % possible all: 81.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→33.98 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7795 / SU ML: 0.82 / σ(F): 1.5 / σ(I): 2.1 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 1268 4.97 %random
Rwork0.1958 ---
all0.1984 26122 --
obs0.1976 25490 97.6 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.835 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 177.09 Å2 / Biso mean: 86.45 Å2 / Biso min: 33.19 Å2
Baniso -1Baniso -2Baniso -3
1--6.4317 Å20 Å2-0 Å2
2--24.7062 Å20 Å2
3----18.2745 Å2
Refinement stepCycle: LAST / Resolution: 2.65→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 0 84 6089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046127
X-RAY DIFFRACTIONf_angle_d0.7488330
X-RAY DIFFRACTIONf_chiral_restr0.05940
X-RAY DIFFRACTIONf_plane_restr0.0031089
X-RAY DIFFRACTIONf_dihedral_angle_d14.0412258
LS refinement shellResolution: 2.65→2.74 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.364 100 -
Rwork0.319 2253 -
all-2364 -
obs-2104 82.8 %
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)
10.80080.5936-0.41380.5367-0.06521.58130.2121-0.2356-1.19440.8898-1.6166-0.73750.98581.1208-0.60960.4938-0.0205-0.34231.33180.010.9766-2.766613.415818.4122
20.4489-0.26420.28240.4464-0.28830.4804-0.0573-0.13970.29350.03510.0124-0.31990.4262-0.1867-0.00490.3742-0.0338-0.08210.4502-0.08330.5728-8.344719.90092.53
31.2726-0.4169-0.74850.3260.49260.6884-0.13960.20980.2223-0.3070.36520.27530.4091-1.23140.72110.4273-0.2582-0.15690.69250.03820.397-31.5159.89124.7992
40.72660.23590.60630.4826-0.52013.44210.08160.4497-0.039-0.241-0.14350.32870.44460.7117-0.10680.6465-0.1635-0.11490.413-0.03840.5202-26.1215-0.6074-5.7945
51.7031-0.5523-0.6130.72730.88791.6911-0.1708-0.295-0.6727-0.48030.1803-0.32670.79870.57170.0251.0268-0.02-0.06470.37060.01240.8241-13.0701-14.7487-0.7237
60.3877-0.4139-0.17630.3367-0.01271.3779-0.0640.12-0.3374-0.0598-0.2775-1.14910.50531.7806-0.00680.98580.3002-0.07440.6427-0.02530.8889-2.1033-11.71494.3446
72.05970.19250.24790.7881-0.14130.1926-0.12810.8208-0.2015-0.52510.243-0.01160.81930.58570.02120.92350.07960.02030.4192-0.16320.556-8.7699-6.9623-12.0383
81.2912-0.4640.2170.57040.28520.38320.1539-0.7205-0.4848-0.02650.146-0.83560.8174-0.0251-0.03670.7697-0.0503-0.03120.3153-0.0290.5375-20.5238-1.4812-2.4115
92.20160.75230.3141.53790.29113.2955-0.37950.6154-0.4577-0.21320.2392-0.14730.6978-0.0996-0.01080.42370.0644-0.0460.2265-0.05180.4492-8.22968.8311-7.6296
100.3027-0.19530.23720.27860.08390.2527-0.1007-0.44430.04740.66720.716-0.36340.94110.268-00.64810.1203-0.11030.65070.09410.60256.679513.38052.0431
110.61320.7240.14580.8189-0.05830.5774-0.46430.17620.1755-0.54820.41-0.36590.0412-0.65580.00620.381-0.0067-0.0090.4433-0.04820.58340.824219.8795-7.6435
120.36490.0006-0.45270.20970.47481.3385-0.82351.4547-1.2021-0.48-0.118-0.08250.48971.3987-0.16420.9399-0.5294-0.12471.3814-0.23690.7717-37.6103-2.9817-0.5479
130.88360.2519-0.21531.52580.25621.9763-0.0847-0.11080.1741-0.01110.15160.22240.1355-0.37480.00240.3715-0.1203-0.03550.70520.05080.4844-29.105410.933713.9788
141.92360.3621-0.33930.80570.04531.1306-0.3271-0.6804-0.0153-0.10050.5618-0.07270.4233-0.04460.18830.6279-0.0205-0.140.47260.27130.4052-10.7768-5.767921.0914
151.15960.14660.38890.0187-0.12641.5178-0.2908-0.7142-1.20360.3920.24520.46251.0306-0.7754-0.06451.0605-0.1407-0.10230.55490.36590.9557-19.4738-19.23914.6926
160.81860.8511-0.28560.83720.34950.823-0.0952-0.5525-0.32630.50950.0364-0.20030.6466-0.1406-0.27820.8676-0.0098-0.09840.83180.30770.5862-17.9914-7.69528.3786
170.34560.564-0.31911.1341-0.82370.65720.2401-0.98510.1286-0.0596-0.1968-0.38770.19741.22230.00190.4115-0.0153-0.11430.67380.10270.406-16.20058.767718.8089
180.8583-0.84210.02311.8791-0.77041.60650.2704-0.7163-0.22120.228-0.07260.81970.2828-1.13330.14690.6995-0.45420.01251.08220.3530.7699-43.1663-5.342925.7049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:27)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 28:58)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 59:83)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 84:105)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 106:145)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 146:175)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 176:253)A0
8X-RAY DIFFRACTION8chain 'A' and (resseq 254:276)A0
9X-RAY DIFFRACTION9chain 'A' and (resseq 277:349)A0
10X-RAY DIFFRACTION10chain 'A' and (resseq 350:369)A0
11X-RAY DIFFRACTION11chain 'A' and (resseq 370:396)A0
12X-RAY DIFFRACTION12chain 'B' and (resseq 3:27)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 28:83)B0
14X-RAY DIFFRACTION14chain 'B' and (resseq 84:145)B0
15X-RAY DIFFRACTION15chain 'B' and (resseq 146:175)B0
16X-RAY DIFFRACTION16chain 'B' and (resseq 176:276)B0
17X-RAY DIFFRACTION17chain 'B' and (resseq 277:307)B0
18X-RAY DIFFRACTION18chain 'B' and (resseq 308:396)B0

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