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- PDB-3ntj: Redox regulation of Plasmodium falciparum ornithine delta-aminotr... -

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Basic information

Entry
Database: PDB / ID: 3ntj
TitleRedox regulation of Plasmodium falciparum ornithine delta-aminotransferase
ComponentsOrnithine aminotransferase
KeywordsTRANSFERASE / ornithine / alpha-ketoglutarate / aminotransferase / PLP-dependent enzyme
Function / homology
Function and homology information


Glutamate and glutamine metabolism / : / ornithine metabolic process / 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) / 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: 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
DepositionJul 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine aminotransferase
B: Ornithine aminotransferase
C: Ornithine aminotransferase
D: Ornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,1138
Polymers188,7294
Non-polymers3844
Water32418
1
A: Ornithine aminotransferase
B: Ornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5564
Polymers94,3642
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-92 kcal/mol
Surface area28660 Å2
MethodPISA
2
C: Ornithine aminotransferase
D: Ornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5564
Polymers94,3642
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-93 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.390, 104.970, 181.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 15:126 or resseq 175:280 or resseq 293:405 )
211chain B and (resseq 15:126 or resseq 175:280 or resseq 293:405 )
311chain C and (resseq 15:126 or resseq 175:280 or resseq 293:405 )
411chain D and (resseq 15:126 or resseq 175:280 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: 3D7 / Gene: OAT, PFF0435w / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6LFH8, ornithine aminotransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 2.2 M amonium sulfate, 100mM citriacidacid, 200m MKCL. Protein concentration in the drop 7.5 mg/ml., pH 8.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979335 Å
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.979335 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 39278 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.094 / Net I/σ(I): 14.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1859 / Rsym value: 0.455 / % possible all: 99.7

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Processing

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

1z7d


Resolution: 3→48.825 Å / SU ML: 0.11 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 2356 6 %
Rwork0.1913 --
obs0.1944 39278 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.949 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.3077 Å2-0 Å20 Å2
2---0.8811 Å20 Å2
3---7.0422 Å2
Refinement stepCycle: LAST / Resolution: 3→48.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12085 0 20 18 12123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912345
X-RAY DIFFRACTIONf_angle_d1.13516714
X-RAY DIFFRACTIONf_dihedral_angle_d17.0864520
X-RAY DIFFRACTIONf_chiral_restr0.0731890
X-RAY DIFFRACTIONf_plane_restr0.0052147
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2584X-RAY DIFFRACTIONPOSITIONAL
12B2584X-RAY DIFFRACTIONPOSITIONAL0.052
13C2584X-RAY DIFFRACTIONPOSITIONAL0.052
14D2584X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.06120.31881370.24652140X-RAY DIFFRACTION100
3.0612-3.12780.28841370.23582155X-RAY DIFFRACTION100
3.1278-3.20050.28371370.23422135X-RAY DIFFRACTION100
3.2005-3.28050.3041390.22522177X-RAY DIFFRACTION100
3.2805-3.36920.2921360.21472130X-RAY DIFFRACTION100
3.3692-3.46830.23321360.2022143X-RAY DIFFRACTION99
3.4683-3.58030.24071370.18412147X-RAY DIFFRACTION100
3.5803-3.70820.25471360.18792124X-RAY DIFFRACTION98
3.7082-3.85660.24791390.18282176X-RAY DIFFRACTION100
3.8566-4.0320.23911370.18192141X-RAY DIFFRACTION99
4.032-4.24450.21881380.17622176X-RAY DIFFRACTION100
4.2445-4.51030.18521380.16452155X-RAY DIFFRACTION100
4.5103-4.85820.21041410.15372209X-RAY DIFFRACTION100
4.8582-5.34660.23591390.16192173X-RAY DIFFRACTION99
5.3466-6.11890.23361400.18152204X-RAY DIFFRACTION100
6.1189-7.70430.22131430.1772240X-RAY DIFFRACTION100
7.7043-48.83180.19281460.18022297X-RAY DIFFRACTION98

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