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- PDB-3it4: The Crystal Structure of Ornithine Acetyltransferase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 3it4
TitleThe Crystal Structure of Ornithine Acetyltransferase from Mycobacterium tuberculosis (Rv1653) at 1.7 A
Components(Arginine biosynthesis bifunctional protein argJ ...) x 2
KeywordsTRANSFERASE / Mycobacterium tuberculosis / Ornithine acetyltransferase / structural genomics / TB Structural Genomics Consortium (TBSGC) / Acyltransferase / Amino-acid biosynthesis / Arginine biosynthesis / Cytoplasm / Multifunctional enzyme
Function / homology
Function and homology information


L-methionine N-acyltransferase activity / glutamate N-acetyltransferase / L-glutamate N-acetyltransferase activity, acting on acetyl-L-ornithine as donor / ornithine biosynthetic process / amino-acid N-acetyltransferase / L-glutamate N-acetyltransferase activity / L-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
ACETATE ION / BENZOIC ACID / Arginine biosynthesis bifunctional protein ArgJ / Arginine biosynthesis bifunctional protein ArgJ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Sep 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: 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)82,85710
Polymers82,3404
Non-polymers5166
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-101 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.140, 99.699, 155.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Arginine biosynthesis bifunctional protein argJ ... , 2 types, 4 molecules ACBD

#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

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Non-polymers , 4 types, 637 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
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 pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2008 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 98245 / Num. obs: 98245 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9834 / % possible all: 96.5

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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: 1.7→35.9 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 2.223 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24371 4899 5 %RANDOM
Rwork0.2044 ---
all0.20637 93276 --
obs0.20637 93276 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5605 0 35 631 6271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215712
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9587789
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91924.312218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36515833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8421539
X-RAY DIFFRACTIONr_chiral_restr0.0910.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214320
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.751.53887
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27726153
X-RAY DIFFRACTIONr_scbond_it2.25131825
X-RAY DIFFRACTIONr_scangle_it3.6584.51636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 327 -
Rwork0.286 6326 -
obs--87.99 %

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