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Yorodumi- PDB-4bif: Biochemical and structural characterisation of a novel manganese-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bif | ||||||
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Title | Biochemical and structural characterisation of a novel manganese- dependent hydroxynitrile lyase from bacteria | ||||||
Components | CUPIN 2 CONSERVED BARREL DOMAIN PROTEIN | ||||||
Keywords | LYASE / METAL-DEPENDENT / MANDELONITRILE / SITE-DIRECTED MUTAGENESIS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | GRANULICELLA TUNDRICOLA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Hajnal, I. / Lyskowski, A. / Hanefeld, U. / Gruber, K. / Schwab, H. / Steiner, K. | ||||||
Citation | Journal: FEBS J. / Year: 2013 Title: Biochemical and Structural Characterisation of a Novel Bacterial Manganese-Dependent Hydroxynitrile Lyase. Authors: Hajnal, I. / Lyskowski, A. / Hanefeld, U. / Gruber, K. / Schwab, H. / Steiner, K. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Crystallization of a Novel Metal-Containing Cupin from Acidobacterium Sp. And Preliminary Diffraction Data Analysis. Authors: Lyskowski, A. / Steiner, K. / Hajnal, I. / Steinkellner, G. / Schwab, H. / Gruber, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bif.cif.gz | 227.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bif.ent.gz | 182.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bif_validation.pdf.gz | 490 KB | Display | wwPDB validaton report |
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Full document | 4bif_full_validation.pdf.gz | 502.3 KB | Display | |
Data in XML | 4bif_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 4bif_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/4bif ftp://data.pdbj.org/pub/pdb/validation_reports/bi/4bif | HTTPS FTP |
-Related structure data
Related structure data | 2f4pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17370.260 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GRANULICELLA TUNDRICOLA (bacteria) / Strain: MP5ACTX9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: E8WYN5 #2: Chemical | ChemComp-MN / #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: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Details: 10%(W/V) PEG 8000, 20%(V/V) ETHYLENE GLYCOL, 0.02 M EACH OF THE AMINO ACIDS DL-ALA, DL-LYS, DL-SER, L-GLU AND GLYCINE, 0.1 M MES IMIDAZOLE BUFFER PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0329 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0329 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→37.72 Å / Num. obs: 48423 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Biso Wilson estimate: 36.67 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.46→2.52 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2F4P Resolution: 2.46→37.722 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 25.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→37.722 Å
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Refine LS restraints |
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LS refinement shell |
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