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- PDB-4nog: Crystal structure of a putative ornithine aminotransferase from T... -

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Basic information

Entry
Database: PDB / ID: 4nog
TitleCrystal structure of a putative ornithine aminotransferase from Toxoplasma gondii ME49 in complex with pyrodoxal-5'-phosphate
ComponentsPutative ornithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / ornithine aminotransferase / Toxoplasma
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
ACETATE ION / BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFilippova, E.V. / Halavaty, A. / Ruan, J. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Ngo, H. / Shanmugam, D. / Roos, D. / Anderson, W.F. ...Filippova, E.V. / Halavaty, A. / Ruan, J. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Ngo, H. / Shanmugam, D. / Roos, D. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Front Cell Infect Microbiol / Year: 2018
Title: CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii .
Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. ...Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. / Moulton, J.D. / Moulton, H. / McPhillie, M.J. / Muench, S.P. / Fishwick, C.W.G. / Sabini, E. / Shanmugam, D. / Roos, D.S. / McLeod, R. / Anderson, W.F. / Ngo, H.M.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Jan 27, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Putative ornithine aminotransferase, mitochondrial
B: Putative ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0819
Polymers98,0562
Non-polymers1,0257
Water18,7541041
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13570 Å2
ΔGint-78 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.190, 61.328, 63.678
Angle α, β, γ (deg.)100.58, 93.23, 107.74
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 Putative ornithine aminotransferase, mitochondrial


Mass: 49027.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGME49_069110, TGME49_269110 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: S8EY38, ornithine aminotransferase

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Non-polymers , 6 types, 1048 molecules

#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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 1041 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Acetate, 0.1 M Bis-Tris, 35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Oct 31, 2013 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.2→62.14 Å / Num. all: 224574 / Num. obs: 224574 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / Num. unique all: 11241 / % possible all: 91

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LG0

3lg0


Resolution: 1.2→62.14 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.639 / SU ML: 0.032 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16494 11260 5 %RANDOM
Rwork0.13322 ---
obs0.13481 213305 90.85 %-
all-213305 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.365 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0.59 Å20.58 Å2
2--0.01 Å21.34 Å2
3----0.73 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.2→62.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 65 1041 7666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0196998
X-RAY DIFFRACTIONr_bond_other_d0.0040.026783
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9799507
X-RAY DIFFRACTIONr_angle_other_deg0.966315614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55223.333309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.555151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2371564
X-RAY DIFFRACTIONr_chiral_restr0.1520.21054
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218029
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021579
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_it4.6621.043521
X-RAY DIFFRACTIONr_mcbond_other4.6612.9783519
X-RAY DIFFRACTIONr_mcangle_it5.5771.5624442
X-RAY DIFFRACTIONr_mcangle_other5.5814443
X-RAY DIFFRACTIONr_scbond_it10.551.5053477
X-RAY DIFFRACTIONr_scbond_other10.551.5053477
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.7752.0715066
X-RAY DIFFRACTIONr_long_range_B_refined8.7779158
X-RAY DIFFRACTIONr_long_range_B_other8.968443
X-RAY DIFFRACTIONr_rigid_bond_restr25.18436986
X-RAY DIFFRACTIONr_sphericity_free24.018537
X-RAY DIFFRACTIONr_sphericity_bonded27.54257258
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 889 -
Rwork0.209 15538 -
obs--90.03 %
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)
17.1533-1.3788-0.62684.9982.55194.47370.05240.2359-0.0866-0.40940.02580.0546-0.276-0.0456-0.07810.049-0.0061-0.01590.01480.00060.021350.442520.639149.0067
20.19960.04840.15810.2560.11940.23880.00150.02630.0116-0.02370.0004-0.0451-0.02730.0348-0.00180.0095-0.0018-0.00150.0308-0.01760.036535.494313.846247.5159
30.0774-0.0332-0.00120.1680.01170.1278-0.0014-0.0066-0.0106-0.0036-0.00010.01590.0089-0.01110.00140.00270.007-0.00670.0318-0.02550.029919.38650.750865.2396
40.6397-1.1589-0.72434.822.97851.93910.10060.0964-0.0165-0.179-0.20370.1032-0.1078-0.16620.1030.02410.0076-0.01150.049-0.02080.038414.69654.815838.1309
50.72320.1074-0.06511.1556-0.08110.7318-0.0260.0879-0.0745-0.07110.006-0.05030.07180.02670.020.01420.0044-0.00290.0459-0.02770.034826.6749-1.360736.5341
60.02160.05130.01022.1593-1.4571.10540.0142-0.02630.06570.1761-0.02250.1991-0.14180.00760.00840.13280.01740.01390.1754-0.06530.228215.815330.939364.0916
74.60985.53953.236511.05933.54285.7354-0.1454-0.17130.18310.106-0.15530.2815-0.3446-0.22320.30070.14820.1137-0.05490.1012-0.03390.082614.307725.060877.6412
80.18590.09890.21010.32550.27210.3435-0.0332-0.02730.0109-0.02670.0050.0203-0.0663-0.02790.02820.04730.0164-0.01190.0382-0.02580.037531.968626.183871.2755
90.05910.05870.00630.153-0.06250.21640.00430.0002-0.01170.0167-0.0078-0.0161-0.00420.02240.00350.00310.0048-0.00720.0289-0.02790.032945.20863.55271.1165
100.90450.2069-0.13710.8124-0.32190.849-0.0228-0.12550.04110.1137-0.00240.0216-0.0462-0.00240.02520.0230.016-0.01260.0376-0.0350.048241.049325.24989.1734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 32
2X-RAY DIFFRACTION2A33 - 102
3X-RAY DIFFRACTION3A103 - 334
4X-RAY DIFFRACTION4A335 - 361
5X-RAY DIFFRACTION5A362 - 439
6X-RAY DIFFRACTION6B17 - 31
7X-RAY DIFFRACTION7B32 - 43
8X-RAY DIFFRACTION8B44 - 101
9X-RAY DIFFRACTION9B102 - 333
10X-RAY DIFFRACTION10B334 - 439

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