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- PDB-5dj9: Crystal structure of the ornithine aminotransferase from Toxoplas... -

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Basic information

Entry
Database: PDB / ID: 5dj9
TitleCrystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with gabaculine
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / inhibitor / complex / parasite / PYRIDOXAL 5'-PHOSPHATE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / 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) / Pyridoxal phosphate-dependent transferase, small 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
3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID / Ornithine aminotransferase
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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: Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with gabaculine
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
DepositionSep 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations / Category: pdbx_database_related / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,74715
Polymers96,7882
Non-polymers1,95913
Water13,079726
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15020 Å2
ΔGint-147 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.258, 60.887, 63.499
Angle α, β, γ (deg.)100.83, 92.38, 107.86
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ornithine aminotransferase, mitochondrial /


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_269110 / Plasmid: pMCSG28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: S8EY38, ornithine aminotransferase

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Non-polymers , 5 types, 739 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-PXG / 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID


Mass: 368.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N2O7P
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350, 5mM gabaculine and 2mM PLP

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 109959 / % possible obs: 96.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.2 / % possible all: 94.7

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Processing

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

4nog


Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.061 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19031 5425 4.9 %RANDOM
Rwork0.15805 ---
obs0.15963 104533 95.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.099 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-1.88 Å2-0.07 Å2
2--1.01 Å20.15 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6524 0 117 726 7367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196818
X-RAY DIFFRACTIONr_bond_other_d0.0020.026528
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9879251
X-RAY DIFFRACTIONr_angle_other_deg1.024315010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5123.487304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.519151147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791560
X-RAY DIFFRACTIONr_chiral_restr0.1090.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217706
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021526
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_it0.6641.2013403
X-RAY DIFFRACTIONr_mcbond_other0.6611.1983400
X-RAY DIFFRACTIONr_mcangle_it1.0521.7954260
X-RAY DIFFRACTIONr_mcangle_other1.0521.7964261
X-RAY DIFFRACTIONr_scbond_it1.181.463415
X-RAY DIFFRACTIONr_scbond_other1.181.463411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8312.1224986
X-RAY DIFFRACTIONr_long_range_B_refined5.51311.7368468
X-RAY DIFFRACTIONr_long_range_B_other5.35910.7228050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.545→1.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 375 -
Rwork0.217 6813 -
obs--84.33 %
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)
12.7211-1.9146-1.19644.0582.96853.60490.16880.240.1045-0.2817-0.104-0.2003-0.30560.1201-0.06480.07770.01220.03930.11560.04160.084451.80921.862448.2984
20.7390.22760.05190.4192-0.230.7056-0.05710.19530.0185-0.12840.03570.01940.02780.02220.02140.08340.0128-0.00140.0912-0.00250.043836.902314.51346.2997
30.56220.2620.06550.59010.03490.3645-0.00970.0072-0.0172-0.00470.01410.09120.0134-0.0577-0.00450.03740.04020.00250.0741-0.00960.115920.83041.634264.5571
40.90820.1111-0.04071.13320.04891.0385-0.15560.261-0.1072-0.34780.14830.09170.1412-0.01980.00720.1664-0.0515-0.02350.1276-0.0350.029124.35780.857338.3141
52.1873-3.4203-0.96026.83211.24542.2667-0.01780.3103-0.0666-0.3997-0.05860.07430.13550.04750.07640.2177-0.0817-0.01790.2174-0.02310.012327.53462.467228.6029
61.21260.1574-2.34420.66120.78816.40290.1325-0.00970.22110.0101-0.01530.201-0.24260.0161-0.11720.08680.06650.01240.06790.00910.207915.292229.432564.9591
70.43860.3680.09810.81390.10040.47170.0361-0.03170.15060.0916-0.03840.1256-0.11610.0160.00220.10910.04710.01840.0576-0.02350.127430.488226.66671.1116
80.4150.05950.14270.4714-0.14510.53880.00220.0101-0.0280.0196-0.0084-0.05750.00510.05770.00620.04920.0482-0.00030.0768-0.01070.104646.55034.622170.5392
90.76220.1274-0.3611.0091-0.17181.24480.0181-0.11740.05230.3206-0.0270.0174-0.21820.13940.00880.18960.00430.00390.0515-0.03520.062642.07626.242687.8969
103.75532.2444-1.51069.58111.29221.19590.4409-0.27320.11230.3567-0.3844-0.0202-0.15360.0343-0.05650.186-0.00310.04910.1102-0.05420.056933.110529.1766104.3419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 32
2X-RAY DIFFRACTION2A33 - 101
3X-RAY DIFFRACTION3A102 - 333
4X-RAY DIFFRACTION4A334 - 418
5X-RAY DIFFRACTION5A419 - 439
6X-RAY DIFFRACTION6B20 - 32
7X-RAY DIFFRACTION7B33 - 102
8X-RAY DIFFRACTION8B103 - 334
9X-RAY DIFFRACTION9B335 - 435
10X-RAY DIFFRACTION10B436 - 440

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