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Yorodumi- PDB-3cvg: Crystal structure of a periplasmic putative metal binding protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cvg | ||||||
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Title | Crystal structure of a periplasmic putative metal binding protein | ||||||
Components | Putative metal binding protein | ||||||
Keywords | METAL BINDING PROTEIN / PSI-II / NYSGXRC / periplasmic / metal binding / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Protein of unknown function DUF3435 / Protein of unknown function (DUF3435) / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein / : Function and homology information | ||||||
Biological species | Coccidioides immitis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 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 periplasmic putative metal binding protein. 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 | 3cvg.cif.gz | 213.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cvg.ent.gz | 178.6 KB | Display | PDB format |
PDBx/mmJSON format | 3cvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cvg_validation.pdf.gz | 471.1 KB | Display | wwPDB validaton report |
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Full document | 3cvg_full_validation.pdf.gz | 513.5 KB | Display | |
Data in XML | 3cvg_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 3cvg_validation.cif.gz | 64.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/3cvg ftp://data.pdbj.org/pub/pdb/validation_reports/cv/3cvg | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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5 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32887.109 Da / Num. of mol.: 4 / Fragment: Residues 22-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coccidioides immitis (fungus) / Strain: RS / Gene: CIMG_05057 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(RIPL) / References: UniProt: Q1DXA6, UniProt: J3KFC8*PLUS #2: Chemical | ChemComp-CA / #3: 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: 2.52 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Bis-tris, PEG 3350, MgCl2, CaCl2, pH 5.5, 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: 0.97958 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 14, 2008 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 103728 / Num. obs: 103728 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 22.6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1 / Num. unique all: 8575 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.97→44.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 80706.96 / 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: 38.3325 Å2 / ksol: 0.331079 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 36.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.97→44.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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