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Yorodumi- PDB-2v4i: Structure of a novel N-acyl-enzyme intermediate of an N-terminal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v4i | ||||||
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Title | Structure of a novel N-acyl-enzyme intermediate of an N-terminal nucleophile (Ntn) hydrolase, OAT2 | ||||||
Components |
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Keywords | TRANSFERASE / CYTOPLASM / ACYL ENZYME / NTN HYDROLASE / ACYLTRANSFERASE / ORNITHINE ACETYL TRANSFERASE | ||||||
Function / homology | Function and homology information glutamate N-acetyltransferase / glutamate N-acetyltransferase activity / ornithine biosynthetic process / L-methionine N-acyltransferase activity / amino-acid N-acetyltransferase / L-glutamate N-acetyltransferase activity / clavulanic acid biosynthetic process / L-arginine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Iqbal, A. / Clifton, I.J. / Schofield, C.J. | ||||||
Citation | Journal: To be Published Title: Structure of a Novel N-Acyl-Enzyme Intermediate of an N-Terminal Nucleophile (Ntn) Hydrolase, Oat2 Authors: Iqbal, A. / Schofield, C.J. / Clifton, I.J. #1: Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v4i.cif.gz | 282.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v4i.ent.gz | 226.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v4i_validation.pdf.gz | 491.4 KB | Display | wwPDB validaton report |
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Full document | 2v4i_full_validation.pdf.gz | 525.7 KB | Display | |
Data in XML | 2v4i_validation.xml.gz | 58.4 KB | Display | |
Data in CIF | 2v4i_validation.cif.gz | 79.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/2v4i ftp://data.pdbj.org/pub/pdb/validation_reports/v4/2v4i | HTTPS FTP |
-Related structure data
Related structure data | 1vz6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 18089.531 Da / Num. of mol.: 4 / Fragment: RESIDUES 8-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12, PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase #2: Protein | Mass: 22846.332 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ACETYLATION OF TERMINAL AMINE OF ALA 181 IN ALL FOUR CHAINS Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12, PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN B, THR 181 TO ALA ENGINEERED RESIDUE IN CHAIN D, THR 181 TO ALA ...ENGINEERED | Sequence details | T181A MUTATION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.54 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 1.4 M AMMONIUM SULPHATE, 0.025 M NACL, 0.1M HEPES-NA PH 7.5, 0.1 M NAG, 20 MM CDCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 14, 2007 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9699 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.471 |
Reflection | Resolution: 2.2→29.7 Å / Num. obs: 79849 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VZ6 Resolution: 2.2→29.7 Å / σ(F): 1.36 / Phase error: 23.9 / Stereochemistry target values: TWIN_LSQ_F Details: TWINNING INFORMATION FRACTION 0.471 OPERATOR H,-K,-L
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.984 Å2 / ksol: 0.343 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.7 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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