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- PDB-5foi: Crystal structure of mycinamicin VIII C21 methyl hydroxylase MycC... -

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Basic information

Entry
Database: PDB / ID: 5foi
TitleCrystal structure of mycinamicin VIII C21 methyl hydroxylase MycCI from Micromonospora griseorubida bound to mycinamicin VIII
ComponentsMYCINAMICIN VIII C21 METHYL HYDROXYLASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Mycinamicin VIII / SPERMIDINE / Mycinamicin VIII C21 methyl hydroxylase
Similarity search - Component
Biological speciesMICROMONOSPORA GRISEORUBIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsDemars, M. / Sheng, F. / Podust, L.M. / Sherman, D.H.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Biochemical and Structural Characterization of Mycci, a Versatile P450 Biocatalyst from the Mycinamicin Biosynthetic Pathway.
Authors: Demars, M.D. / Sheng, F. / Park, S.R. / Lowell, A.N. / Podust, L.M. / Sherman, D.H.
History
DepositionNov 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYCINAMICIN VIII C21 METHYL HYDROXYLASE
B: MYCINAMICIN VIII C21 METHYL HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,33211
Polymers91,4642
Non-polymers2,8689
Water2,648147
1
A: MYCINAMICIN VIII C21 METHYL HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4768
Polymers45,7321
Non-polymers1,7447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MYCINAMICIN VIII C21 METHYL HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8563
Polymers45,7321
Non-polymers1,1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.781, 59.516, 74.623
Angle α, β, γ (deg.)83.20, 72.15, 62.61
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MYCINAMICIN VIII C21 METHYL HYDROXYLASE / 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

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Non-polymers , 5 types, 156 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MY8 / Mycinamicin VIII


Mass: 507.702 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H49NO6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsSPERMIDINE (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

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 % / Description: NONE
Crystal growpH: 7
Details: 20% PEG 3350, 0.2 M CA ACETATE, 20 MM SPERMIDINE, 0.84 MM TCEP, pH 7

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESERCH / Detector: CCD / Date: Sep 3, 2015 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.21→71 Å / Num. obs: 36326 / % possible obs: 91.1 % / Observed criterion σ(I): 0.5 / Redundancy: 2 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 3.8
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 1.9 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.3 / % possible all: 71.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CV9

3cv9


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
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1838 5.1 %RANDOM
Rwork0.18227 ---
obs0.18572 34383 90.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.168 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0.15 Å2-0.78 Å2
2---1.47 Å20.37 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.21→71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6013 0 200 147 6360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196365
X-RAY DIFFRACTIONr_bond_other_d0.0010.026163
X-RAY DIFFRACTIONr_angle_refined_deg1.9072.018692
X-RAY DIFFRACTIONr_angle_other_deg1.353.01314084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6722.472271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64915992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.161566
X-RAY DIFFRACTIONr_chiral_restr0.1090.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217122
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8632.6743111
X-RAY DIFFRACTIONr_mcbond_other1.8622.6743110
X-RAY DIFFRACTIONr_mcangle_it2.8864.013887
X-RAY DIFFRACTIONr_mcangle_other2.8864.013888
X-RAY DIFFRACTIONr_scbond_it2.0032.8223254
X-RAY DIFFRACTIONr_scbond_other2.0022.8223255
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1334.1514806
X-RAY DIFFRACTIONr_long_range_B_refined4.8721.3287251
X-RAY DIFFRACTIONr_long_range_B_other4.8721.3317252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 86 -
Rwork0.255 1706 -
obs--60.7 %

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