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- PDB-3it6: The Crystal Structure of Ornithine Acetyltransferase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3it6
TitleThe Crystal Structure of Ornithine Acetyltransferase complexed with Ornithine from Mycobacterium tuberculosis (Rv1653) at 2.4 A
Components
  • Arginine biosynthesis bifunctional protein argJ alpha chain
  • Arginine biosynthesis bifunctional protein argJ beta chain
KeywordsTRANSFERASE / Mycobacterium tuberculosis / Ornithine acetyltransferase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium (TBSGC) / Acyltransferase / Amino-acid biosynthesis / Arginine biosynthesis / Multifunctional enzyme
Function / homology
Function and homology information


ornithine biosynthetic process / glutamate N-acetyltransferase / glutamate N-acetyltransferase activity / acetyl-CoA:L-glutamate N-acetyltransferase activity / methione N-acyltransferase activity / amino-acid N-acetyltransferase / arginine biosynthetic process / cytoplasm
Similarity search - Function
arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) ...arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) / 4-Layer Sandwich / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-ornithine / Arginine biosynthesis bifunctional protein ArgJ / Arginine biosynthesis bifunctional protein ArgJ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSankaranarayanan, R. / Cherney, M.M. / Garen, C. / Garen, G. / Yuan, M. / James, M.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The molecular structure of ornithine acetyltransferase from Mycobacterium tuberculosis bound to ornithine, a competitive inhibitor.
Authors: Sankaranarayanan, R. / Cherney, M.M. / Garen, C. / Garen, G. / Niu, C. / Yuan, M. / James, M.N.
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 4, 2014Group: Data collection
Revision 1.3Sep 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: Arginine biosynthesis bifunctional protein argJ alpha chain
B: Arginine biosynthesis bifunctional protein argJ beta chain
C: Arginine biosynthesis bifunctional protein argJ alpha chain
D: Arginine biosynthesis bifunctional protein argJ beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6056
Polymers82,3404
Non-polymers2642
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15810 Å2
ΔGint-104 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.849, 100.095, 156.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arginine biosynthesis bifunctional protein argJ alpha chain / Glutamate N-acetyltransferase / Ornithine acetyltransferase / OATase / Ornithine transacetylase


Mass: 19981.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: argJ, MT1691, MTCY06H11.18, Rv1653 / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli)
References: UniProt: P63571, UniProt: P9WPZ3*PLUS, glutamate N-acetyltransferase
#2: Protein Arginine biosynthesis bifunctional protein argJ beta chain / Amino-acid acetyltransferase / N-acetylglutamate synthase / AGS


Mass: 21188.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: argJ, Rv1653, MT1691, MTCY06H11.18 / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli)
References: UniProt: P63571, UniProt: P9WPZ3*PLUS, amino-acid N-acetyltransferase
#3: Chemical ChemComp-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein concentration 13.5 mg/mL in 2.5 mM HEPES pH 7.5, Precipitant 0.02 M MgCl2, 22% polyacrylic acid 5100 in 0.1 M HEPES at pH 7.5, 3mM ornithine in mother liquor used to soak the ...Details: Protein concentration 13.5 mg/mL in 2.5 mM HEPES pH 7.5, Precipitant 0.02 M MgCl2, 22% polyacrylic acid 5100 in 0.1 M HEPES at pH 7.5, 3mM ornithine in mother liquor used to soak the crystal, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2008
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 38018 / Num. obs: 38018 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3755 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0055refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VZ6

1vz6


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.869 / SU B: 8.66 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26695 1887 5 %RANDOM
Rwork0.20955 ---
obs0.21241 35958 99.1 %-
all-35958 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.093 Å2
Baniso -1Baniso -2Baniso -3
1-5.19 Å20 Å20 Å2
2---2.53 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5684 0 18 404 6106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215780
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.9557888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7045792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00524.234222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84615850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3221540
X-RAY DIFFRACTIONr_chiral_restr0.0740.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214386
X-RAY DIFFRACTIONr_mcbond_it0.4221.53940
X-RAY DIFFRACTIONr_mcangle_it0.81126244
X-RAY DIFFRACTIONr_scbond_it1.27531840
X-RAY DIFFRACTIONr_scangle_it2.1714.51644
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 137 -
Rwork0.267 2628 -
obs--99.35 %

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