+Open data
-Basic information
Entry | Database: PDB / ID: 2y4d | |||||||||
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Title | X-ray crystallographic structure of E. coli apo-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 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 | 2y4d.cif.gz | 176.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y4d.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 2y4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y4d_validation.pdf.gz | 489.2 KB | Display | wwPDB validaton report |
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Full document | 2y4d_full_validation.pdf.gz | 503.2 KB | Display | |
Data in XML | 2y4d_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 2y4d_validation.cif.gz | 53.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4d ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4d | HTTPS FTP |
-Related structure data
Related structure data | 2y4eC 2y4fC 2gvkS 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 612 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-GOL / #6: 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: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 11, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→60 Å / Num. obs: 58929 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 8 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GVK Resolution: 2→35 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 4.483 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.187 / 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: 29.754 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35 Å
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Refine LS restraints |
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