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- PDB-1vz6: Ornithine Acetyltransferase (ORF6 Gene Product - Clavulanic Acid ... -

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Basic information

Entry
Database: PDB / ID: 1vz6
TitleOrnithine Acetyltransferase (ORF6 Gene Product - Clavulanic Acid Biosynthesis) from Streptomyces clavuligerus
ComponentsORNITHINE ACETYL-TRANSFERASE
KeywordsTRANSFERASE / ORNITHINE ACETYLTRANSFERASE / CLAVULANIC ACID / N-ACETYL-ORNITHINE / N-ACETYL-GLUTAMATE / ANTIBIOTIC
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 / clavulanic acid biosynthetic process / L-glutamate N-acetyltransferase activity / L-arginine biosynthetic process / cytoplasm
Similarity search - Function
ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / 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 / Alpha Beta
Similarity search - Domain/homology
Glutamate N-acetyltransferase Oat2 / Arginine biosynthesis bifunctional protein ArgJ 3
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsElkins, J.M. / Kershaw, N.J. / Schofield, C.J.
CitationJournal: Biochem.J. / Year: 2005
Title: X-Ray Crystal Structure of Ornithine Acetyltransferase from the Clavulanic Acid Biosynthesis Gene Cluster.
Authors: Elkins, J.M. / Kershaw, N.J. / Schofield, C.J.
History
DepositionMay 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORNITHINE ACETYL-TRANSFERASE
B: ORNITHINE ACETYL-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6916
Polymers83,3072
Non-polymers3844
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.663, 94.444, 180.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.00308, -0.00028), (-0.00297, 0.9834, -0.1814), (0.00083, -0.1814, -0.98341)
Vector: 91.6386, 17.70978, 191.77954)

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Components

#1: Protein ORNITHINE ACETYL-TRANSFERASE


Mass: 41653.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase
#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.: 71 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 180 AND 181, DUE TO THE AUTO-PROTEOLYTIC SELF- ...THERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 180 AND 181, DUE TO THE AUTO-PROTEOLYTIC SELF-ACTIVATION OF THE ENZYME

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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: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 8
Details: PROTEIN AT 12MG/ML MIXED 1:1 WITH A SOLUTION OF: 1.2M (NH4)2SO4, 40MM NH4H2PO4, 0.1M TRIS PH 8.0, 6% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.75→32.11 Å / Num. obs: 29114 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 5.5
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→32.08 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1769009.77 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2737 5 %RANDOM
Rwork0.212 ---
obs0.212 54604 99.9 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.37743 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--23.65 Å20 Å2
3----23.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.75→32.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 20 71 5503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.632
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.662.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 463 5.1 %
Rwork0.277 8694 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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