+Open data
-Basic information
Entry | Database: PDB / ID: 2wnh | ||||||
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Title | Crystal Structure Analysis of Klebsiella sp ASR1 Phytase | ||||||
Components | 3-PHYTASE | ||||||
Keywords | HYDROLASE / HISTIDINE ACID PHOSPHATASE | ||||||
Function / homology | Function and homology information 3-phytase / 3-phytase activity / sugar-phosphatase activity / acid phosphatase activity / lysosome organization / outer membrane-bounded periplasmic space / lysosome / metal ion binding Similarity search - Function | ||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å | ||||||
Authors | Bohm, K. / Mueller, J.J. / Heinemann, U. | ||||||
Citation | Journal: FEBS J. / Year: 2010 Title: Crystal Structure of Klebsiella Sp. Asr1 Phytase Suggests Substrate Binding to a Preformed Active Site that Meets the Requirements of a Plant Rhizosphere Enzyme. Authors: Bohm, K. / Herter, T. / Mueller, J.J. / Borriss, R. / Heinemann, U. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wnh.cif.gz | 177.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wnh.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wnh_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 2wnh_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 2wnh_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 2wnh_validation.cif.gz | 56.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/2wnh ftp://data.pdbj.org/pub/pdb/validation_reports/wn/2wnh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 46115.301 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-421 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Strain: ASR1 / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q84CN9, 3-phytase #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, VAL 139 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 295 TO SER ...ENGINEERED | |
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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | Details: 4 M SODIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8984 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 14, 2004 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8984 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→94.49 Å / Num. obs: 113622 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.65→1.75 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.6 / % possible all: 72.9 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.68→94.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.906 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.091 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.288 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→94.49 Å
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Refine LS restraints |
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