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- PDB-5eav: Unliganded structure of the ornithine aminotransferase from Toxop... -

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Basic information

Entry
Database: PDB / ID: 5eav
TitleUnliganded structure of the ornithine aminotransferase from Toxoplasma gondii
ComponentsOrnithine aminotransferase, mitochondrial, putative
KeywordsTRANSFERASE / PLP / gabaculine / parasite / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / ornithine aminotransferase / ornithine aminotransferase activity / : / L-proline biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function
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) ...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
DI(HYDROXYETHYL)ETHER / Ornithine aminotransferase
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFilippova, E.V. / Minasov, G. / Flores, K. / Le, H.V. / Silverman, R.B. / McLeod, R.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Unliganded structure of the ornithine aminotransferase from Toxoplasma gondii
Authors: Filippova, E.V. / Minasov, G. / Flores, K. / Le, H.V. / Silverman, R.B. / McLeod, R.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ornithine aminotransferase, mitochondrial, putative
B: Ornithine aminotransferase, mitochondrial, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,67311
Polymers96,7882
Non-polymers8859
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-76 kcal/mol
Surface area27820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.338, 61.067, 63.597
Angle α, β, γ (deg.)100.88, 92.23, 108.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ornithine aminotransferase, mitochondrial, putative


Mass: 48394.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_069110 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: S8EY38, ornithine aminotransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350, 0.5 mM oxidized glutathione

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 6, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 97272 / % possible obs: 93.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 32.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.86 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NOG

4nog


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.134 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4794 4.9 %RANDOM
Rwork0.177 ---
obs0.178 92446 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å2-1.84 Å2-0.64 Å2
2--2.3 Å20.8 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 49 544 7128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196780
X-RAY DIFFRACTIONr_bond_other_d0.0010.026526
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9769187
X-RAY DIFFRACTIONr_angle_other_deg0.949315011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4835857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6423.42307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.131151157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3611562
X-RAY DIFFRACTIONr_chiral_restr0.1150.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.0217691
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021523
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9421.3253410
X-RAY DIFFRACTIONr_mcbond_other0.941.3243409
X-RAY DIFFRACTIONr_mcangle_it1.4261.9844273
X-RAY DIFFRACTIONr_mcangle_other1.4261.9844274
X-RAY DIFFRACTIONr_scbond_it1.5411.5813370
X-RAY DIFFRACTIONr_scbond_other1.541.5813370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3092.2854915
X-RAY DIFFRACTIONr_long_range_B_refined5.066.6588187
X-RAY DIFFRACTIONr_long_range_B_other5.066.668188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å
RfactorNum. reflection% reflection
Rfree0.241 313 -
Rwork0.232 6115 -
obs--83.42 %
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)
11.96660.12430.29970.7956-0.48431.1726-0.02560.3821-0.0315-0.2051-0.0589-0.13580.08280.2190.08450.08460.02340.05160.1604-0.00350.039245.346515.42847.9453
20.96420.3279-0.28750.6718-0.31581.0089-0.06070.14710.1528-0.03950.06310.1539-0.0631-0.0853-0.00240.04990.0116-0.00440.06280.00590.079323.584819.050957.9459
31.35480.07890.19330.47140.08260.78830.0244-0.0122-0.29970.0617-0.00410.01190.1108-0.0648-0.02040.06480.00470.03870.0411-0.02220.140323.9289-5.999469.2587
41.08920.7959-0.07671.2145-0.1930.422-0.17810.2299-0.0396-0.16010.1530.1406-0.001-0.09330.02510.0463-0.01730.00420.1054-0.03850.083314.97632.925556.6836
52.28791.2167-0.52662.7569-0.8672.3381-0.71890.7667-0.3872-0.83990.602-0.17170.4765-0.07320.1170.3712-0.24080.11360.3839-0.16570.087926.2831.569837.1508
62.0860.9515-0.28682.8284-0.90350.65510.1103-0.13860.48020.16-0.00880.3505-0.0185-0.1661-0.10150.12850.04180.08540.1397-0.0490.232713.722525.8372.6241
70.69010.1478-0.28711.28460.23041.09310.00280.0540.14870.0408-0.03680.0788-0.1610.01360.03390.0860.01510.01250.0556-0.00940.091834.342125.570865.6502
81.01140.06970.21510.4884-0.0810.5330.0187-0.0462-0.11280.048-0.0057-0.05420.07590.0127-0.01290.06340.03380.01670.0478-0.00830.067741.0159-0.320775.0041
90.50790.1105-0.01030.6922-0.24130.7328-0.0160.03110.00180.0472-0.053-0.1067-0.06450.15150.0690.0490.00950.00790.0795-0.01420.080346.950610.850972.0138
101.72740.0716-0.32252.1845-0.50822.5027-0.0442-0.28460.11020.6807-0.01560.0744-0.41990.1790.05970.3222-0.00940.02750.1032-0.06260.067137.767527.225791.6027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 60
2X-RAY DIFFRACTION2A61 - 136
3X-RAY DIFFRACTION3A137 - 203
4X-RAY DIFFRACTION4A204 - 370
5X-RAY DIFFRACTION5A371 - 439
6X-RAY DIFFRACTION6B20 - 50
7X-RAY DIFFRACTION7B51 - 120
8X-RAY DIFFRACTION8B121 - 214
9X-RAY DIFFRACTION9B215 - 343
10X-RAY DIFFRACTION10B344 - 440

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