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- PDB-5e3k: Crystal structure of the ornithine aminotransferase from Toxoplas... -

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Basic information

Entry
Database: PDB / ID: 5e3k
TitleCrystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid
ComponentsAminotransferase
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) ...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
Chem-5JV / CARBONATE ION / DI(HYDROXYETHYL)ETHER / Ornithine aminotransferase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 (S)-4-amino-5-fluoropentanoic acid
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 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,64817
Polymers96,7882
Non-polymers1,85915
Water14,646813
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-148 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.328, 61.524, 63.555
Angle α, β, γ (deg.)100.72, 92.96, 108.18
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 Aminotransferase / Ornithine aminotransferase / mitochondrial


Mass: 48394.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (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, 828 molecules

#2: Chemical ChemComp-5JV / 4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid


Mass: 344.257 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17N2O7P
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97913 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 84366 / % possible obs: 97.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.9 / % possible all: 95.7

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Processing

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

4nog


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.49 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19601 4228 5 %RANDOM
Rwork0.15374 ---
obs0.1559 80138 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-1.64 Å2-0.83 Å2
2--1.04 Å2-0.5 Å2
3---1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 114 813 7487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196928
X-RAY DIFFRACTIONr_bond_other_d0.0020.026649
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9839394
X-RAY DIFFRACTIONr_angle_other_deg1.041315297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94523.366309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.598151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7391563
X-RAY DIFFRACTIONr_chiral_restr0.1080.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217871
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021554
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_it0.6721.2853457
X-RAY DIFFRACTIONr_mcbond_other0.6721.2853456
X-RAY DIFFRACTIONr_mcangle_it1.0391.9254344
X-RAY DIFFRACTIONr_mcangle_other1.0381.9264345
X-RAY DIFFRACTIONr_scbond_it1.1821.5183471
X-RAY DIFFRACTIONr_scbond_other1.1821.5183471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8072.25051
X-RAY DIFFRACTIONr_long_range_B_refined5.46712.3428682
X-RAY DIFFRACTIONr_long_range_B_other5.46712.3428682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 256 -
Rwork0.216 5229 -
obs--84.7 %
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)
12.0251-1.1888-0.48523.71171.86427.13830.21410.26520.0666-0.2559-0.1435-0.2628-0.39170.0017-0.07060.07140.01140.04710.09470.02610.073750.020921.902149.4672
20.66870.09730.36860.4007-0.17991.14440.00290.1901-0.0255-0.1520.0023-0.0072-0.00510.079-0.00520.0880.01220.02920.0788-0.00570.056435.678913.60947.1023
30.60440.32180.03610.8861-0.07960.57540.00910.0123-0.0407-0.00230.03840.0625-0.0001-0.1282-0.04740.01750.02120.01060.06150.0080.063919.47370.876965.2252
40.33660.1910.06930.77880.16551.097-0.0080.0905-0.0759-0.22870.02320.01430.1084-0.0004-0.01520.11330.0249-0.00230.057-0.0150.057322.9451-0.016138.8511
51.6981-2.7847-0.80017.24292.20721.8176-0.01380.16550.003-0.44940.00870.0038-0.01430.03540.00510.136-0.0179-0.00290.072-0.00150.003626.03421.782529.2604
62.30370.4132-0.67360.50790.18570.4140.18420.10160.52620.062-0.10170.2333-0.044-0.0969-0.08250.11560.10490.07830.2061-0.04890.291615.253529.410769.1708
70.80610.47730.19931.12310.14380.77510.0889-0.05460.1390.1569-0.0390.074-0.27-0.0154-0.04980.17390.03360.04940.0548-0.00880.088431.032425.86471.5766
80.44950.01950.1630.4369-0.17560.72170.0260.0029-0.070.0161-0.0081-0.11730.00450.0885-0.01790.02480.02460.00440.0435-0.00640.101245.21193.698671.1971
90.8081-0.1562-0.59780.4125-0.25283.160.0092-0.12940.12760.11630.0562-0.0803-0.13160.185-0.06540.1402-0.0457-0.01720.0566-0.02530.061947.927326.149487.9864
100.78990.0327-0.3981.4790.10211.78630.0148-0.15840.05350.25140.03160.0081-0.20180.0457-0.04640.1430.0010.02360.0411-0.02250.02537.380925.021990.4374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 32
2X-RAY DIFFRACTION2A33 - 101
3X-RAY DIFFRACTION3A102 - 334
4X-RAY DIFFRACTION4A335 - 418
5X-RAY DIFFRACTION5A419 - 439
6X-RAY DIFFRACTION6B17 - 41
7X-RAY DIFFRACTION7B42 - 101
8X-RAY DIFFRACTION8B102 - 334
9X-RAY DIFFRACTION9B335 - 366
10X-RAY DIFFRACTION10B367 - 440

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