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Yorodumi- PDB-3cmn: Crystal structure of a putative hydrolase with a novel fold from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cmn | ||||||
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Title | Crystal structure of a putative hydrolase with a novel fold from Chloroflexus aurantiacus | ||||||
Components | Putative hydrolase | ||||||
Keywords | HYDROLASE / PSI-II / NYSGXRC / Putative hydrolase / apoenzyme / helical protein / 10492m / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Zincin-like metallopeptidase, N-terminal domain / Zinicin-like metallopeptidase type 2 / Conserved hypothetical protein CHP03883, F420 biosynthesis associated / Zinicin-like metallopeptidase type 2, N-terminal / Zincin-like metallopeptidase / Lysin / Up-down Bundle / Mainly Alpha / Uncharacterized protein Function and homology information | ||||||
Biological species | Chloroflexus aurantiacus J-10-fl (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||
Authors | Agarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative hydrolase with a novel fold from Chloroflexus aurantiacus. Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cmn.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cmn.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/3cmn ftp://data.pdbj.org/pub/pdb/validation_reports/cm/3cmn | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42698.551 Da / Num. of mol.: 1 / Fragment: Residues 30-388 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aurantiacus J-10-fl (bacteria) Species: Chloroflexus aurantiacus / Strain: J-10-fl / DSM 635 / Gene: Caur_0242 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: A9WCA2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 1.5 M Sodium chloride, 10% Ethanol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9795 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 18, 2008 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 17996 / Num. obs: 17996 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 24.4 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1 / Num. unique all: 1693 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→49.34 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 60793.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.0922 Å2 / ksol: 0.371968 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→49.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
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Xplor file |
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