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Yorodumi- PDB-2vzk: Structure of the acyl-enzyme complex of an N-terminal nucleophile... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vzk | ||||||||||||
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Title | Structure of the acyl-enzyme complex of an N-terminal nucleophile (Ntn) hydrolase, OAT2 | ||||||||||||
Components |
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Keywords | TRANSFERASE / ACYL ENZYME / NTN HYDROLASE / ACYLTRANSFERASE | ||||||||||||
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 / clavulanic acid biosynthetic process / L-glutamate N-acetyltransferase activity / arginine biosynthetic process / cytoplasm Similarity search - Function | ||||||||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||||||||
Authors | Iqbal, A. / Clifton, I.J. / Schofield, C.J. | ||||||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Anatomy of a Simple Acyl Intermediate in Enzyme Catalysis: Combined Biophysical and Modeling Studies on Ornithine Acetyl Transferase. Authors: Iqbal, A. / Clifton, I.J. / Bagonis, M. / Kershaw, N.J. / Domene, C. / Claridge, T.D. / Wharton, C.W. / Schofield, C.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 | 2vzk.cif.gz | 552 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vzk.ent.gz | 459.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/2vzk ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vzk | HTTPS FTP |
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-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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2 |
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3 |
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4 |
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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
-Protein , 1 types, 4 molecules ACEG
#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 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase |
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-GLUTAMATE N-ACETYLTRANSFERASE 2 BETA ... , 2 types, 4 molecules BDFH
#2: Protein | Mass: 22834.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase |
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#3: Protein | Mass: 22876.357 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: ACETYLISATION OF THR 181 IN CHAINS D, F, AND H / Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase |
-Non-polymers , 3 types, 296 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.12 % / Description: NONE |
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Crystal grow | Temperature: 290 K / pH: 7.5 Details: 1.4M AMMONIUM SULPHATE, 100MM N-ACETYL-L-GLUTAMATE, 200MM NACL, 100MM TRIS HCL PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 29, 2007 / Details: MONTEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→37 Å / Num. obs: 62183 / % possible obs: 94.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.33→2.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.03 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VZ6, CHAIN A Resolution: 2.33→171.5 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.91 / SU B: 19.81 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.587 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED FROM TLS MODEL BY TLSANL
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.038 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→171.5 Å
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Refine LS restraints |
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