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Yorodumi- PDB-3cu3: Crystal structure of a domain of unknown function with a cystatin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cu3 | ||||||
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Title | Crystal structure of a domain of unknown function with a cystatin-like fold (npun_r1993) from nostoc punctiforme pcc 73102 at 2.00 A resolution | ||||||
Components | Domain of unknown function with a cystatin-like fold | ||||||
Keywords | METAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information Domain of unknown function DUF4440 / Domain of unknown function (DUF4440) / Steroid delta5-4-isomerase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Nostoc punctiforme (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Domain of Unknown Function with a Cystatin-like Fold (ZP_00107529.1) from Nostoc punctiforme PCC 73102 at 2.00 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cu3.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cu3.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 3cu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cu3_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 3cu3_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 3cu3_validation.xml.gz | 10 KB | Display | |
Data in CIF | 3cu3_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/3cu3 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/3cu3 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 19358.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00107529.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: D0VWT9*PLUS | ||||||||
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#2: Chemical | ChemComp-MG / | ||||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Has protein modification | Y | Sequence details | 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.47 Details: NANODROP, 0.2M Magnesium chloride, 36.0% PEG 400, 0.1M HEPES pH 7.47, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97905, 0.97929 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 17, 2008 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→29.386 Å / Num. obs: 14803 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.61 % / Biso Wilson estimate: 17.709 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7.97 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→29.386 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.161 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.142 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. MG ION AND POLYETHYLENE GLYCOL MOLECULE FROM CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE STRUCTURE. ETHYLENE GLYCOL MOLECULES FROM CRYO SOLUTION ARE ALSO MODELED IN THIS STRUCTURE.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.479 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.386 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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