+Open data
-Basic information
Entry | Database: PDB / ID: 2yeq | ||||||
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Title | Structure of PhoD | ||||||
Components | ALKALINE PHOSPHATASE D | ||||||
Keywords | HYDROLASE / PHOSPHODIESTERASE | ||||||
Function / homology | Function and homology information alkaline phosphatase / alkaline phosphatase activity / acid phosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å | ||||||
Authors | Lillington, J.E.D. / Rodriguez, F. / Roversi, P. / Johnson, S.J. / Berks, B. / Lea, S.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal Structure of the Bacillus Subtilis Phosphodiesterase Phod Reveals an Iron and Calcium-Containing Active Site. Authors: Rodriguez, F. / Lillington, J. / Johnson, S. / Timmel, C.R. / Lea, S.M. / Berks, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yeq.cif.gz | 253.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yeq.ent.gz | 200.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yeq_validation.pdf.gz | 6.6 MB | Display | wwPDB validaton report |
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Full document | 2yeq_full_validation.pdf.gz | 6.6 MB | Display | |
Data in XML | 2yeq_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 2yeq_validation.cif.gz | 69.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/2yeq ftp://data.pdbj.org/pub/pdb/validation_reports/ye/2yeq | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 3 / Auth seq-ID: 1 - 520 / Label seq-ID: 1 - 520
NCS oper:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59785.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P42251, alkaline phosphatase |
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-Non-polymers , 7 types, 712 molecules
#2: Chemical | ChemComp-PE5 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NA / #5: Chemical | #6: Chemical | ChemComp-CA / #7: Chemical | #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: 3.94 Å3/Da / Density % sol: 0.28 % / Description: MAD USING SIGNAL FROM FE |
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Crystal grow | pH: 5.8 / Details: 0.1 NA/K PO4 PH 5.8, 52% PEG 200, 0.2M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2818 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 2, 2010 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2818 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→135 Å / Num. obs: 141401 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.93→135.64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.65 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY
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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: 23.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→135.64 Å
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Refine LS restraints |
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