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- PDB-1z7d: Ornithine aminotransferase PY00104 from Plasmodium Yoelii -

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Basic information

Entry
Database: PDB / ID: 1z7d
TitleOrnithine aminotransferase PY00104 from Plasmodium Yoelii
Componentsornithine aminotransferase
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / malaria / plasmodium yoelii / ornithine aminotransferase
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
Ornithine aminotransferase
Similarity search - Component
Biological speciesPlasmodium yoelii yoelii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Alam, Z. / Amani, M. / Lew, J. / Wasney, G. / Boulanger, K. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...Walker, J.R. / Alam, Z. / Amani, M. / Lew, J. / Wasney, G. / Boulanger, K. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Hui, R. / Vedadi, M. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionMar 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ornithine aminotransferase
B: ornithine aminotransferase
C: ornithine aminotransferase
D: ornithine aminotransferase
E: ornithine aminotransferase
F: ornithine aminotransferase


Theoretical massNumber of molelcules
Total (without water)290,1466
Polymers290,1466
Non-polymers00
Water9,458525
1
A: ornithine aminotransferase
B: ornithine aminotransferase


Theoretical massNumber of molelcules
Total (without water)96,7152
Polymers96,7152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-51 kcal/mol
Surface area27950 Å2
MethodPISA
2
C: ornithine aminotransferase
D: ornithine aminotransferase


Theoretical massNumber of molelcules
Total (without water)96,7152
Polymers96,7152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-53 kcal/mol
Surface area27920 Å2
MethodPISA
3
E: ornithine aminotransferase
F: ornithine aminotransferase


Theoretical massNumber of molelcules
Total (without water)96,7152
Polymers96,7152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-50 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.489, 221.829, 114.484
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ornithine aminotransferase


Mass: 48357.664 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii yoelii (eukaryote) / Species: Plasmodium yoelii / Strain: yoelii / Production host: Escherichia coli (E. coli) / References: UniProt: Q7RT90, ornithine aminotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.6 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 298 K / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 25, 2005
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 158741 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OAT

2oat


Resolution: 2.1→49.74 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.714 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25885 7970 5 %RANDOM
Rwork0.21483 ---
obs0.21703 150728 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å21.03 Å2
2--0.77 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17647 0 0 525 18172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02217969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.98424325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88452236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2725.421784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.922153267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9581566
X-RAY DIFFRACTIONr_chiral_restr0.0980.22793
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213309
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.29045
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.212392
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2859
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.604311501
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.498418112
X-RAY DIFFRACTIONr_scbond_it3.20657248
X-RAY DIFFRACTIONr_scangle_it4.62776213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.143 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 533 -
Rwork0.251 10249 -
obs--91.06 %

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