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- PDB-1vz8: Ornithine Acetyltransferase (ORF6 Gene Product - Clavulanic Acid ... -

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Basic information

Entry
Database: PDB / ID: 1vz8
TitleOrnithine Acetyltransferase (ORF6 Gene Product - Clavulanic Acid Biosynthesis) from Streptomyces clavuligerus (SeMet structure)
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 / MAD / 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
C: ORNITHINE ACETYL-TRANSFERASE
D: ORNITHINE ACETYL-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,69110
Polymers168,1154
Non-polymers5766
Water77543
1
A: ORNITHINE ACETYL-TRANSFERASE
B: ORNITHINE ACETYL-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4426
Polymers84,0582
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ORNITHINE ACETYL-TRANSFERASE
D: ORNITHINE ACETYL-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2504
Polymers84,0582
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.792, 180.194, 73.326
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99997, -0.00815, 0.00094), (0.0082, -0.99546, 0.09481), (0.00017, 0.09482, 0.99549)57.38302, 2.1122, -0.07507
2given(0.99996, 0.00794, -0.0038), (-0.00827, 0.99556, -0.09374), (0.00303, 0.09377, 0.99559)0.87747, -6.54977, -36.80755
3given(-0.99974, -0.02144, -0.00757), (0.02133, -0.99968, 0.01364), (-0.00786, 0.01347, 0.99988)58.44386, -5.54532, -36.41934

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Components

#1: Protein
ORNITHINE ACETYL-TRANSFERASE


Mass: 42028.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE-SUBSTITUTED / 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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 45.4 %
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: ESRF / Beamline: BM14 / Wavelength: 0.89
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 2.75→20.5 Å / Num. obs: 40839 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.9
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.75→23.67 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1847476.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2047 5 %RANDOM
Rwork0.235 ---
obs0.235 40847 99.9 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.380215 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-13.73 Å20 Å2-1.02 Å2
2---10.1 Å20 Å2
3----3.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.75→23.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10778 0 30 43 10851
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
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_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 336 4.9 %
Rwork0.277 6452 -
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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