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Yorodumi- PDB-1q9u: Crystal structure of uncharacterized conserved protein DUF302 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q9u | ||||||
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Title | Crystal structure of uncharacterized conserved protein DUF302 from Bacillus stearothermophilus | ||||||
Components | Uncharacterized protein APC35924 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Zn-binding proteins / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / autoSHARP/wARP / Resolution: 1.8 Å | ||||||
Authors | Kim, Y. / Li, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure analysis of Zinc-binding, uncharacterized protein from Bacillus stearothermophilus Authors: Kim, Y. / Li, H. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN. IT COULD BE EITHER A DIMER OR A HEXAMER (A TRIMER OF DIMERS). | ||||||
Remark 999 | SEQUENCE THERE WAS NO SEQUENCE DATABASE REFERENCE FOR THE PROTEIN AT THE TIME OF PROCESSING. THE N- ...SEQUENCE THERE WAS NO SEQUENCE DATABASE REFERENCE FOR THE PROTEIN AT THE TIME OF PROCESSING. THE N-TERMINAL RESIDUES SER-ASN-ALA ARE CLONING ARTIFACTS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q9u.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q9u.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 1q9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q9u_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 1q9u_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 1q9u_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1q9u_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/1q9u ftp://data.pdbj.org/pub/pdb/validation_reports/q9/1q9u | HTTPS FTP |
-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: 14725.053 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: APC35924 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KY88*PLUS #2: Chemical | ChemComp-ZN / #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: 1.91 Å3/Da / Density % sol: 35.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1,4,-butanedial, imidazole, Zn(OAc)2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28322, 0.97932 | |||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Aug 6, 2003 / Details: mirrors | |||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. all: 21413 / Num. obs: 21413 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 6.6 | |||||||||
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: autoSHARP/wARP / Resolution: 1.8→43.43 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.5561 Å2 / ksol: 0.344162 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→43.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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