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- PDB-4aw3: Structure of the mixed-function P450 MycG F286V mutant in complex... -

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Basic information

Entry
Database: PDB / ID: 4aw3
TitleStructure of the mixed-function P450 MycG F286V mutant in complex with mycinamicin V in P1 space group
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
PROTOPORPHYRIN IX CONTAINING FE / MYCINAMICIN V / Mycinamicin IV hydroxylase/epoxidase
Similarity search - Component
Biological speciesMICROMONOSPORA GRISEORUBIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLi, S. / Tietz, D.R. / Rutaganira, F.U. / Kells, P.M. / Anzai, Y. / Kato, F. / Pochapsky, T.C. / 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
DepositionMay 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Dec 5, 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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: P-450-LIKE PROTEIN
B: P-450-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,81118
Polymers93,0172
Non-polymers3,79416
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-171.2 kcal/mol
Surface area30810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.455, 56.107, 76.422
Angle α, β, γ (deg.)90.43, 97.22, 102.11
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 P-450-LIKE PROTEIN / MYCG


Mass: 46508.719 Da / Num. of mol.: 2 / 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, 534 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MYV / MYCINAMICIN V


Mass: 711.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H61NO12
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 286 TO VAL ENGINEERED RESIDUE IN CHAIN B, PHE 286 TO VAL
Nonpolymer detailsMYCINAMICIN V (MYV): NATIVE MYCG SUBSTRATE PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE ...MYCINAMICIN V (MYV): NATIVE MYCG SUBSTRATE PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE BOND TO CYS 346 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: 2.51 Å3/Da / Density % sol: 50.9 % / Description: NONE
Crystal growpH: 6.5
Details: 1.6 M AMMONIUM SULFATE, 0.1 M MES PH6.5, 10% V/V 1,4-DIOXANE

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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: Feb 27, 2012 / 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: 2.05→75.77 Å / Num. obs: 54108 / % possible obs: 96.6 % / Observed criterion σ(I): 1.5 / Redundancy: 2.1 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.1
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / % possible all: 95.7

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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 2Y98

2y98


Resolution: 2.05→75.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.7 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 2752 5.1 %RANDOM
Rwork0.1659 ---
obs0.16934 51252 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-1.15 Å2-0.08 Å2
2--0.06 Å2-0.72 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.05→75.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6124 0 250 518 6892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226685
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0282.069151
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1525800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54322.282298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2721583
X-RAY DIFFRACTIONr_chiral_restr0.1360.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215089
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_it1.1091.53988
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96826424
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4232697
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3024.52727
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 207 -
Rwork0.251 3688 -
obs--95.02 %

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