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- PDB-2wi9: Selective oxidation of carbolide C-H bonds by engineered macrolid... -

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Basic information

Entry
Database: PDB / ID: 2wi9
TitleSelective oxidation of carbolide C-H bonds by engineered macrolide P450 monooxygenase
ComponentsCYTOCHROME P450 HYDROXYLASE PIKC
KeywordsOXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / CYP107L1 / CYTOCHROME P450 / HEME / IRON / MACROLIDE MONOOXYGENASE / METAL-BINDING / MONOOXYGENASE / OXIDOREDUCTASE ANTIBIOTIC BIOSYNTHESIS / PIKC
Function / homology
Function and homology information


pikromycin synthase / macrolide 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
Chem-1D2 / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 monooxygenase PikC
Similarity search - Component
Biological speciesSTREPTOMYCES VENEZUELAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, S. / Chaulagain, M.R. / Knauff, A.R. / Podust, L.M. / Montgomery, J. / Sherman, D.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Selective Oxidation of Carbolide C-H Bonds by an Engineered Macrolide P450 Mono-Oxygenase.
Authors: Li, S. / Chaulagain, M.R. / Knauff, A.R. / Podust, L.M. / Montgomery, J. / Sherman, D.H.
History
DepositionMay 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / 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 / _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: CYTOCHROME P450 HYDROXYLASE PIKC
B: CYTOCHROME P450 HYDROXYLASE PIKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5689
Polymers96,3632
Non-polymers2,2047
Water10,377576
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A: CYTOCHROME P450 HYDROXYLASE PIKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1403
Polymers48,1821
Non-polymers9582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME P450 HYDROXYLASE PIKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4286
Polymers48,1821
Non-polymers1,2465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.254, 109.094, 153.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99993, -0.01215, 0.00056), (-0.01197, 0.9912, 0.13182), (-0.00216, 0.13181, -0.99127)
Vector: 74.86146, -9.10812, 72.46054)

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Components

#1: Protein CYTOCHROME P450 HYDROXYLASE PIKC / PIKC


Mass: 48181.641 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: O87605
#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-1D2 / CYCLODODECYL 3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSIDE


Mass: 341.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H39NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 50 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 50 TO ASN
Sequence details20 N-TERMINAL RESIDUES INCLUDING 6XHIS TAG ARE 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: 2.74 Å3/Da / Density % sol: 55.1 % / Description: NONE
Crystal growpH: 7.5 / Details: 15% PEG 4000, 0.1 M TRIS-HCL, PH 7.5; 200 MM MGCL2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 2, 2007 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 68456 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 87.7 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.7 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C6H

2c6h


Resolution: 2→88.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.931 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 6789 10.1 %RANDOM
Rwork0.184 ---
obs0.189 60321 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--1.65 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2→88.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6102 0 149 576 6827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226578
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9832.0319018
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9722.153288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.112151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5211576
X-RAY DIFFRACTIONr_chiral_restr0.1370.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215079
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_it1.2131.54051
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06126523
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.22232527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9734.52493
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→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 400 -
Rwork0.241 3744 -
obs--83.35 %

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