- PDB-5foi: Crystal structure of mycinamicin VIII C21 methyl hydroxylase MycC... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5foi
Title
Crystal structure of mycinamicin VIII C21 methyl hydroxylase MycCI from Micromonospora griseorubida bound to mycinamicin VIII
Components
MYCINAMICIN VIII C21 METHYL HYDROXYLASE
Keywords
OXIDOREDUCTASE
Function / homology
Function and homology information
Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / monooxygenase activity / iron ion binding / heme binding Similarity search - Function
MYCINAMICINVIIIC21METHYLHYDROXYLASE / CYTOCHROME P450 MYCCI / MYCINAMICIN BIOSYNTHESIS PROTEIN CI / MYCCI
Mass: 45732.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ENGINEERED SEQUENCE AT THE N-TERMINUS / Source: (gene. exp.) MICROMONOSPORA GRISEORUBIDA (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: Q83WF5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
SPERMIDINE (SPD): PART OF CRYSTALLIZATION CONDITIONS MYCINAMICIN VIII (MY8): NATURAL SUBSTRATE OF ...SPERMIDINE (SPD): PART OF CRYSTALLIZATION CONDITIONS MYCINAMICIN VIII (MY8): NATURAL SUBSTRATE OF MYCCI PROTOPORPHYRIN IX CONTAINING FE (HEM): LINKED VIA THIOLATE BOND TO CYS 337 GLYCEROL (GOL): CRYO-PROTECTANT
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.34 Å3/Da / Density % sol: 47.4 % / Description: NONE
Crystal grow
pH: 7 Details: 20% PEG 3350, 0.2 M CA ACETATE, 20 MM SPERMIDINE, 0.84 MM TCEP, pH 7
Resolution: 2.21→71 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.238 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2515
1838
5.1 %
RANDOM
Rwork
0.18227
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obs
0.18572
34383
90.81 %
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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