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- PDB-2xbk: X-ray structure of the substrate-bound cytochrome P450 PimD - a p... -

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Basic information

Entry
Database: PDB / ID: 2xbk
TitleX-ray structure of the substrate-bound cytochrome P450 PimD - a polyene macrolide antibiotic pimaricin epoxidase
ComponentsPIMD PROTEIN
KeywordsOXIDOREDUCTASE / EPOXIDATION
Function / homology
Function and homology information


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 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 4,5-DE-EPOXYPIMARICIN / PimD protein
Similarity search - Component
Biological speciesSTREPTOMYCES NATALENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKells, P.M. / Ouellet, H. / Santos-Aberturas, J. / Aparicio, J.F. / Podust, L.M.
CitationJournal: Chem.Biol. / Year: 2010
Title: Structure of Cytochrome P450 Pimd Suggests Epoxidation of the Polyene Macrolide Pimaricin Occurs Via a Hydroperoxoferric Intermediate.
Authors: Kells, P.M. / Ouellet, H. / Santos-Aberturas, J. / Aparicio, J.F. / Podust, L.M.
History
DepositionApr 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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 / 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: PIMD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7953
Polymers44,5291
Non-polymers1,2662
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.920, 99.690, 58.505
Angle α, β, γ (deg.)90.00, 111.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PIMD PROTEIN


Mass: 44528.770 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-397
Source method: isolated from a genetically manipulated source
Details: RESIDUES UPSTREAM OF SER 5 INCLUDING 6XHIS TAG ARE ENGINEERED
Source: (gene. exp.) STREPTOMYCES NATALENSIS (bacteria) / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q9EW92
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-XBK / 4,5-DE-EPOXYPIMARICIN


Mass: 649.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H47NO12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details4,5-DEEPOXYPIMARICIN: NON-EPOXIDATED PRECURSOR OF THE POLYENE ANTIBIOTIC PIMARICIN OR NATAMYCIN. ...4,5-DEEPOXYPIMARICIN: NON-EPOXIDATED PRECURSOR OF THE POLYENE ANTIBIOTIC PIMARICIN OR NATAMYCIN. FORMED FROM XBK, THE POLYENE MACROCYCLE, AND XBL, MYCOSAMINE SUGAR PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND TO CYS 346
Sequence details6XHIS TAG ENGINEERED AT THE N-TERMINUS UPSTREAM OF SER 5

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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: 2.87 Å3/Da / Density % sol: 57.2 % / Description: NONE
Crystal growTemperature: 296 K / pH: 7
Details: 0.2 M SODIUM MALONATE, PH 7.0; 20% PEG 3330, T=23 C

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2009 / 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: 1.95→17.01 Å / Num. obs: 38650 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X9P

2x9p


Resolution: 1.95→67.88 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.439 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES WITH THE SIDE CHAIN MISSING FROM THE ELECTRON DENSITY WERE MODELED AS ALANINE
RfactorNum. reflection% reflectionSelection details
Rfree0.21396 1912 4.9 %RANDOM
Rwork0.14977 ---
obs0.15286 36749 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.816 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å2-0.12 Å2
2---0.09 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.95→67.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 89 272 3367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9852.0424557
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2675419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61622.649151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95915530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8081539
X-RAY DIFFRACTIONr_chiral_restr0.140.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212622
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_it1.8961.52045
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.97523305
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.05231280
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.3594.51252
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.77733325
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 151 -
Rwork0.264 2700 -
obs--99.86 %

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