+Open data
-Basic information
Entry | Database: PDB / ID: 2y4e | |||||||||
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Title | X-ray crystallographic structure of E. coli ppix-EfeB | |||||||||
Components | PEROXIDASE YCDB | |||||||||
Keywords | OXIDOREDUCTASE / IRON UPTAKE / DYP-PEROXIDASE-LIKE / DEFERROCHELATASE | |||||||||
Function / homology | Function and homology information protoporphyrin ferrochelatase / iron import into cell / ferrochelatase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / heme binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Bamford, V.A. / Andrews, S.C. / Watson, K.A. | |||||||||
Citation | Journal: To be Published Title: Efeb, the Peroxidase Component of the Efeuob Bacterial Fe(II) Transport System, Also Shows Novel Removal of Iron from Heme Authors: Bamford, V.A. / Andrews, S.C. / Watson, K.A. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y4e.cif.gz | 168.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y4e.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 2y4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y4e_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2y4e_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2y4e_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 2y4e_validation.cif.gz | 46.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4e ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4e | HTTPS FTP |
-Related structure data
Related structure data | 2y4dSC 2y4fC C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 44890.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PET-46 EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P31545, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Temperature: 291 K / pH: 7 Details: 2.0M AMMONIUM SULFATE, 5% (V/V) PEG 400, 0.1M HEPES PH 7.0, 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.968 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 11, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→60 Å / Num. obs: 36837 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y4D Resolution: 2.3→48.8 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.601 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.29 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.545 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.8 Å
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