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Yorodumi- PDB-3vnr: Co-crystal structure of NRPS adenylation protein CytC1 with amino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vnr | ||||||
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Title | Co-crystal structure of NRPS adenylation protein CytC1 with aminobutyric acid and AMP from streptomyces | ||||||
Components | NRPS adenylation protein CytC1 | ||||||
Keywords | LIGASE / Acetyl-CoA synthetase-like / adenylation / ATP Binding | ||||||
Function / homology | ANL, C-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / ALPHA-AMINOBUTYRIC ACID / ADENOSINE MONOPHOSPHATE Function and homology information | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Okumura, H. / Ueki, M. / Shiro, Y. / Osada, H. | ||||||
Citation | Journal: To be Published Title: Substrate recognition mechanism of NRPS adenylation protein from Streptomyces Authors: Ueki, M. / Okumura, H. / Osada, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vnr.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vnr.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/3vnr ftp://data.pdbj.org/pub/pdb/validation_reports/vn/3vnr | HTTPS FTP |
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-Related structure data
Related structure data | 3vnqC 3vnsC 1amuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 58992.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: RK95-74 / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-ABA / |
#4: Water | ChemComp-HOH / |
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.1M ammonium sulfate, 24-32% PEG5000 monomethyl ether, 1mM ATP, 100mM Hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 64664 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.8 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 74.126 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 16.8 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 6.643 / Rsym value: 0.474 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AMU Resolution: 1.75→35.11 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.21 / σ(F): 0 / Phase error: 20.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.268 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.15 Å2 / Biso mean: 26.7731 Å2 / Biso min: 10.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→35.11 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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