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- PDB-4zlv: Crystal structure of the ornithine aminotransferase from Toxoplas... -

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Basic information

Entry
Database: PDB / ID: 4zlv
TitleCrystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with the Schiff base between PLP and Lys286
ComponentsOrnithine aminotransferase, mitochondrial, putative
KeywordsTRANSFERASE / Structural Genomics / pyridoxal 5'-phosphate (PLP)-independent aminotransferase / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-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
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFilippova, E.V. / Minasov, G. / Flores, K. / Van Le, H. / Silverman, R.B. / McLeod, R. / 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 the Schiff base between PLP and Lys286
Authors: Filippova, E.V. / Minasov, G. / Flores, K. / Van Le, H. / Silverman, R.B. / McLeod, R. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)97,96511
Polymers96,7882
Non-polymers1,1779
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-142 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.481, 61.459, 63.435
Angle α, β, γ (deg.)100.45, 92.39, 108.32
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 19 - 439 / Label seq-ID: 19 - 439

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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_269110 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: S8EY38, ornithine aminotransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / 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: 0.97889 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 70729 / Num. obs: 70729 / % possible obs: 96 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5 / % possible all: 87.4

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
HKL-3000phasing
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0107refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NGO

4ngo


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.978 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20591 3490 4.9 %RANDOM
Rwork0.16191 67239 --
obs0.16408 67239 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-2.64 Å2-0.62 Å2
2--1.29 Å2-0.53 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6533 0 67 503 7103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196745
X-RAY DIFFRACTIONr_bond_other_d0.0020.026467
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.989139
X-RAY DIFFRACTIONr_angle_other_deg1314874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3215847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10923.576302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.143151143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3031558
X-RAY DIFFRACTIONr_chiral_restr0.0950.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217617
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021501
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_it0.7571.7433385
X-RAY DIFFRACTIONr_mcbond_other0.7571.7423384
X-RAY DIFFRACTIONr_mcangle_it1.2252.614233
X-RAY DIFFRACTIONr_mcangle_other1.2252.6114234
X-RAY DIFFRACTIONr_scbond_it1.1311.9763360
X-RAY DIFFRACTIONr_scbond_other1.1231.9713356
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7162.894901
X-RAY DIFFRACTIONr_long_range_B_refined5.72715.3588041
X-RAY DIFFRACTIONr_long_range_B_other5.67514.7527822
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6462 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.455
loose thermal1.5110
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 216 -
Rwork0.285 4444 -
obs--85.3 %
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)
11.16470.3206-0.02670.692-0.14871.3112-0.06530.47910.0816-0.16480.0096-0.0591-0.05690.11540.05570.0771-0.0465-0.01050.3110.10040.045638.435215.278647.4935
21.44820.28570.02021.0919-0.10230.6794-0.00410.1022-0.12970.0314-0.0020.15140.0024-0.1070.0060.0625-0.0397-0.00910.17140.04080.095119.44981.313865.4659
31.5493-0.7309-0.98116.10622.17252.3243-0.38140.54220.0552-0.58830.3580.33150.1115-0.36240.02340.2766-0.1844-0.09090.42390.03130.038116.40642.646237.2306
42.09851.1117-0.64032.1466-0.65442.913-0.62020.6921-0.2581-0.69760.4985-0.19780.5306-0.05450.12170.319-0.21580.09270.4588-0.10940.036727.1138-0.761837.2019
52.53040.8097-0.00662.62270.06882.89580.1452-0.02830.48260.1979-0.12160.4551-0.3966-0.1009-0.02360.1181-0.0090.07640.11140.02350.1715.103124.933971.4839
61.5078-0.191-0.45961.72420.09581.2690.02570.15070.24910.1548-0.0944-0.0267-0.26260.08470.06870.1294-0.0753-0.03550.13260.09910.100336.828323.341565.2673
71.3450.01590.33740.8338-0.19260.84330.00990.0081-0.12630.1423-0.048-0.1381-0.0010.11420.03810.0919-0.0401-0.03810.17230.08590.091445.37873.099173.4976
82.508-0.7475-2.10271.5767-0.64228.1366-0.129-0.29560.36080.43270.0324-0.3482-0.23620.69030.09660.3501-0.1253-0.13280.1491-0.01710.148147.663126.929786.7028
92.1241-0.4989-0.2692.882-0.52083.0565-0.111-0.35760.15930.95140.0437-0.0456-0.60650.24010.06730.5089-0.0781-0.03690.1079-0.01140.030336.972225.847590.3155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 101
2X-RAY DIFFRACTION2A102 - 334
3X-RAY DIFFRACTION3A335 - 365
4X-RAY DIFFRACTION4A366 - 439
5X-RAY DIFFRACTION5B19 - 49
6X-RAY DIFFRACTION6B50 - 125
7X-RAY DIFFRACTION7B126 - 332
8X-RAY DIFFRACTION8B333 - 366
9X-RAY DIFFRACTION9B367 - 440

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