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- PDB-3lg0: Structure of Plasmodium falciparum ornithine delta-aminotransferase -

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Basic information

Entry
Database: PDB / ID: 3lg0
TitleStructure of Plasmodium falciparum ornithine delta-aminotransferase
ComponentsOrnithine aminotransferase
KeywordsTRANSFERASE / Activation of Plasmodium falciparum ornithine delta-aminotransferase / delta-aminotransferase / pyridoxal-5-phosphate-dependent enzyme / ornithine / alpha-ketoglutarate / Plasmodium falciparum / Aminotransferase / Pyridoxal phosphate
Function / homology
Function and homology information


: / ornithine aminotransferase activity / ornithine aminotransferase / L-proline biosynthetic process / pyridoxal phosphate 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
Ornithine aminotransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFritz-Wolf, K. / Jortzik, E. / Stumpf, M. / Becker, K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Redox regulation of Plasmodium falciparum ornithine delta-aminotransferase.
Authors: Jortzik, E. / Fritz-Wolf, K. / Sturm, N. / Hipp, M. / Rahlfs, S. / Becker, K.
History
DepositionJan 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 16, 2014Group: Other
Revision 1.3Sep 6, 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


Theoretical massNumber of molelcules
Total (without water)188,7294
Polymers188,7294
Non-polymers00
Water7,206400
1
A: Ornithine aminotransferase
B: Ornithine aminotransferase


Theoretical massNumber of molelcules
Total (without water)94,3642
Polymers94,3642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-49 kcal/mol
Surface area28040 Å2
MethodPISA
2
C: Ornithine aminotransferase
D: Ornithine aminotransferase


Theoretical massNumber of molelcules
Total (without water)94,3642
Polymers94,3642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-49 kcal/mol
Surface area28060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.530, 106.930, 147.140
Angle α, β, γ (deg.)90.00, 91.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN D AND (RESSEQ 15:140 OR RESSEQ 175:282 OR RESSEQ 293:405 )
211CHAIN B AND (RESSEQ 15:140 OR RESSEQ 175:282 OR RESSEQ 293:405 )
311CHAIN C AND (RESSEQ 15:140 OR RESSEQ 175:282 OR RESSEQ 293:405 )
411CHAIN A AND (RESSEQ 15:140 OR RESSEQ 175:282 OR RESSEQ 293:405 )

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Components

#1: Protein
Ornithine aminotransferase / / Ornithine-oxo-acid aminotransferase


Mass: 47182.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate CDC / Honduras / Gene: OAT / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q07805, ornithine aminotransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.9 M lithium chloride, 0.1 M citric acid, 20 % PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98696 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 28, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98696 Å / Relative weight: 1
ReflectionResolution: 2.3→43.4 Å / Num. all: 69479 / Num. obs: 66243 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 45.4 Å2 / Rsym value: 0.05 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 7.6 / Rsym value: 0.13 / % possible all: 10

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHENIXmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1z7d

1z7d


Resolution: 2.3→43.375 Å / SU ML: 0.3 / Isotropic thermal model: overall / σ(F): 2 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 3975 6 %
Rwork0.2033 --
obs0.2061 66225 95.34 %
all-69479 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.677 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2086 Å20 Å23.0067 Å2
2---0.2172 Å2-0 Å2
3----7.3084 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12070 0 0 400 12470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712314
X-RAY DIFFRACTIONf_angle_d1.08416673
X-RAY DIFFRACTIONf_dihedral_angle_d16.244508
X-RAY DIFFRACTIONf_chiral_restr0.0741889
X-RAY DIFFRACTIONf_plane_restr0.0042146
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D2710X-RAY DIFFRACTIONPOSITIONAL
12B2710X-RAY DIFFRACTIONPOSITIONAL0.042
13C2710X-RAY DIFFRACTIONPOSITIONAL0.041
14A2710X-RAY DIFFRACTIONPOSITIONAL0.036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32810.30351040.26871636X-RAY DIFFRACTION72
2.3281-2.35760.32331210.25951893X-RAY DIFFRACTION82
2.3576-2.38860.30831410.26582201X-RAY DIFFRACTION94
2.3886-2.42130.34961450.26412276X-RAY DIFFRACTION97
2.4213-2.45590.28151400.25432201X-RAY DIFFRACTION97
2.4559-2.49260.29691470.25162302X-RAY DIFFRACTION97
2.4926-2.53150.33391450.25462257X-RAY DIFFRACTION97
2.5315-2.5730.32861410.24812218X-RAY DIFFRACTION97
2.573-2.61740.26451450.23372268X-RAY DIFFRACTION97
2.6174-2.66490.29331440.24072256X-RAY DIFFRACTION97
2.6649-2.71620.32761440.25762258X-RAY DIFFRACTION97
2.7162-2.77160.30471430.23682238X-RAY DIFFRACTION97
2.7716-2.83190.29831460.23642290X-RAY DIFFRACTION97
2.8319-2.89770.29021440.22362255X-RAY DIFFRACTION97
2.8977-2.97020.28481460.22512296X-RAY DIFFRACTION97
2.9702-3.05050.29541430.2232230X-RAY DIFFRACTION97
3.0505-3.14020.28331450.2292278X-RAY DIFFRACTION97
3.1402-3.24160.28031430.21352230X-RAY DIFFRACTION97
3.2416-3.35740.25471460.21022300X-RAY DIFFRACTION97
3.3574-3.49170.23391440.20052248X-RAY DIFFRACTION97
3.4917-3.65060.22861460.19522283X-RAY DIFFRACTION97
3.6506-3.84290.2471440.18372258X-RAY DIFFRACTION97
3.8429-4.08350.23991460.18072288X-RAY DIFFRACTION98
4.0835-4.39850.20681440.16162264X-RAY DIFFRACTION97
4.3985-4.84070.17441460.14692278X-RAY DIFFRACTION97
4.8407-5.53990.18381470.16192308X-RAY DIFFRACTION97
5.5399-6.9750.22421450.18172268X-RAY DIFFRACTION96
6.975-43.38310.18171400.16372172X-RAY DIFFRACTION91

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