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- PDB-3zsn: Structure of the mixed-function P450 MycG F286A mutant in complex... -

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Basic information

Entry
Database: PDB / ID: 3zsn
TitleStructure of the mixed-function P450 MycG F286A mutant in complex with mycinamicin IV
ComponentsP-450-LIKE PROTEIN
KeywordsOXIDOREDUCTASE / MYCINAMICIN BIOSYNTHESIS
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
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
BENZAMIDINE / PROTOPORPHYRIN IX CONTAINING FE / MYCINAMICIN IV / Mycinamicin IV hydroxylase/epoxidase
Similarity search - Component
Biological speciesMICROMONOSPORA GRISEORUBIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, S. / Kells, P.M. / Rutaganira, F.U. / Anzai, Y. / Kato, F. / Sherman, D.H. / Podust, L.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Substrate Recognition by the Multifunctional Cytochrome P450 Mycg in Mycinamicin Hydroxylation and Epoxidation Reactions.
Authors: Li, S. / Tietz, D.R. / Rutaganira, F.U. / Kells, P.M. / Anzai, Y. / Kato, F. / Pochapsky, T.C. / Sherman, D.H. / Podust, L.M.
History
DepositionJun 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: 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 / pdbx_struct_special_symmetry / 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: P-450-LIKE PROTEIN
B: P-450-LIKE PROTEIN
C: P-450-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,50420
Polymers139,4423
Non-polymers5,06217
Water18,3931021
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A: P-450-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1897
Polymers46,4811
Non-polymers1,7096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: P-450-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2187
Polymers46,4811
Non-polymers1,7376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: P-450-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0976
Polymers46,4811
Non-polymers1,6175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.214, 100.940, 440.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-1398-

BEN

21C-1398-

BEN

31C-1398-

BEN

41C-2343-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein P-450-LIKE PROTEIN / MYCG


Mass: 46480.668 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MICROMONOSPORA GRISEORUBIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59523

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Non-polymers , 5 types, 1038 molecules

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


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MIV / MYCINAMICIN IV


Mass: 695.880 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H61NO11
#4: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 286 TO ALA ENGINEERED RESIDUE IN CHAIN B, PHE 286 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, PHE 286 TO ALA ENGINEERED RESIDUE IN CHAIN B, PHE 286 TO ALA ENGINEERED RESIDUE IN CHAIN C, PHE 286 TO ALA
Nonpolymer detailsPROTOPORPHYRIN IX (HEM): HEME THIOLATE BOND TO CYS 346 BENZAMIDINE (BEN): ADDITIVE MYCINAMICIN IV ...PROTOPORPHYRIN IX (HEM): HEME THIOLATE BOND TO CYS 346 BENZAMIDINE (BEN): ADDITIVE MYCINAMICIN IV (MIV): NATIVE MYCG SUBSTRATE GLYCEROL (GOL): CRYO-PROTECTANT
Sequence detailsTHE 6XHIS TAG AND THROMBIN CLEAVAGE SITE ARE ENGINEERED AT THE N-TERMINUS. F286A MUTATION IS ENGINEERED.

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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: 2.4 Å3/Da / Density % sol: 48.9 % / Description: NONE
Crystal growpH: 5
Details: 2.5% PEG 1500; 0.1 M SODIUM MALONATE, PH 5.0; 2% BENZAMIDINE.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESEARCH / Detector: CCD / Date: May 28, 2011 / 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: 1.9→146.95 Å / Num. obs: 91500 / % possible obs: 89.2 % / Observed criterion σ(I): 1.5 / Redundancy: 5.4 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.7 / % possible all: 64.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y4H

2y4h
PDB Unreleased entry


Resolution: 1.9→220.42 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.753 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24497 4576 5 %RANDOM
Rwork0.18522 ---
obs0.18818 86665 88.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→220.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9234 0 354 1021 10609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0229970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9022.04113619
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74551212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39222.278461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.061151584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.73715130
X-RAY DIFFRACTIONr_chiral_restr0.1260.21506
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217727
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.111.56009
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.89529702
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.08533961
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8244.53917
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 223 -
Rwork0.422 3880 -
obs--54.08 %

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