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Yorodumi- PDB-1rxq: YfiT from Bacillus subtilis is a probable metal-dependent hydrola... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rxq | ||||||
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Title | YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology | ||||||
Components | yfiT | ||||||
Keywords | METAL BINDING PROTEIN / Nickel-binding / hydrolase / helix-bundle / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / metal-binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Rajan, S.S. / Yang, X. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: YfiT from Bacillus subtilis Is a Probable Metal-Dependent Hydrolase with an Unusual Four-Helix Bundle Topology Authors: Rajan, S.S. / Yang, X. / Shuvalova, L. / Collart, F. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rxq.cif.gz | 161.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rxq.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 1rxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rxq_validation.pdf.gz | 521.3 KB | Display | wwPDB validaton report |
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Full document | 1rxq_full_validation.pdf.gz | 535.7 KB | Display | |
Data in XML | 1rxq_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 1rxq_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxq ftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxq | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg label comp-ID: ILE / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 10 - 178 / Label seq-ID: 10 - 178
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 20885.986 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yfiT / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: GenBank: 16077906, UniProt: O31562*PLUS |
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-Non-polymers , 7 types, 479 molecules
#2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-GLU / | #4: Chemical | #5: Chemical | ChemComp-ALA / | #6: Chemical | ChemComp-THR / | #7: Chemical | ChemComp-GLY / | #8: 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: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate, 23% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 4, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 75437 / Num. obs: 70594 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.085 / Rsym value: 0.072 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.7→1.744 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.21 / % possible all: 67.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.36 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.271 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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