- PDB-2y4f: X-ray crystallographic structure of E. coli heme-EfeB -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2y4f
Title
X-ray crystallographic structure of E. coli heme-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
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.
Resolution: 2.7→60 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.858 / SU B: 14.684 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28449
1209
5.1 %
RANDOM
Rwork
0.19323
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obs
0.19779
22545
97.72 %
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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