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Yorodumi- PDB-3cyg: Crystal structure of an uncharacterized protein from Fervidobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cyg | ||||||
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Title | Crystal structure of an uncharacterized protein from Fervidobacterium nodosum Rt17-B1 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Uncharacterized Protein / PSI-II / 10495j / Fervibacterium nodosum / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Fervidobacterium nodosum Rt17-B1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å | ||||||
Authors | Damodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an uncharacterized protein from Fervidobacterium nodosum Rt17-B1. Authors: Damodharan, L. / 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 | 3cyg.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cyg.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 3cyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cyg_validation.pdf.gz | 432.9 KB | Display | wwPDB validaton report |
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Full document | 3cyg_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 3cyg_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 3cyg_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/3cyg ftp://data.pdbj.org/pub/pdb/validation_reports/cy/3cyg | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 26480.303 Da / Num. of mol.: 2 / Fragment: Residues 37-247 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fervidobacterium nodosum Rt17-B1 (bacteria) Species: Fervidobacterium nodosum / Strain: Rt17-B1 / DSM 5306 / Gene: Fnod_1146 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(RIPL) / References: UniProt: A7HM60 #2: 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: 2.41 Å3/Da / Density % sol: 49.05 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG 3500, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2008 / Details: Mirrors |
Radiation | Monochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→50 Å / Num. all: 15697 / Num. obs: 15697 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 68.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.61→2.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1 / Num. unique all: 883 / % possible all: 54.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.61→36.53 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 69967.1 / 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: 28.1183 Å2 / ksol: 0.29191 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.61→36.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.61→2.76 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file |
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