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- PDB-2jjo: Structure of cytochrome P450 EryK in complex with its natural sub... -

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Basic information

Entry
Database: PDB / ID: 2jjo
TitleStructure of cytochrome P450 EryK in complex with its natural substrate erD
ComponentsCYTOCHROME P450 113A1
KeywordsOXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING / ANTIBIOTIC BIOSYNTHESIS / TIE-ROD MECHANISM OF ACTION / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


erythromycin 12-hydroxylase / macrolide biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / monooxygenase activity / NADP binding / 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
Erythromycin D / PROTOPORPHYRIN IX CONTAINING FE / Erythromycin C-12 hydroxylase
Similarity search - Component
Biological speciesSACCHAROPOLYSPORA ERYTHRAEA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSavino, C. / Sciara, G. / Miele, A.E. / Kendrew, S.G. / Vallone, B.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Investigating the Structural Plasticity of a Cytochrome P450: Three-Dimensional Structures of P450 Eryk and Binding to its Physiological Substrate.
Authors: Savino, C. / Montemiglio, L.C. / Sciara, G. / Miele, A.E. / Kendrew, S.G. / Jemth, P. / Gianni, S. / Vallone, B.
History
DepositionApr 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 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 113A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6673
Polymers45,3471
Non-polymers1,3202
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.840, 36.526, 96.004
Angle α, β, γ (deg.)90.00, 93.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYTOCHROME P450 113A1 / CYTOCROME P450 CYP113A1 / ERYTHROMYCIN B/D C-12 HYDROXYLASE


Mass: 45347.031 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROPOLYSPORA ERYTHRAEA (bacteria) / Strain: NRRL 23338 / Description: CDNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR
References: UniProt: P48635, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#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-EY5 / Erythromycin D


Mass: 703.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H65NO12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 1 TO LEU

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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: 2.05 Å3/Da / Density % sol: 39.6 %
Crystal growpH: 8.5
Details: 25% PEG 3350, 0.2M AMMONIUM ACETATE, 0.1M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 27953 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 2→2.15 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 10.9 / % possible all: 80.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JJN

2jjn


Resolution: 1.99→95.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.99 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1281 5 %RANDOM
Rwork0.163 ---
obs0.167 24282 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-0.54 Å2
2--0.06 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.99→95.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 92 335 3477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223260
X-RAY DIFFRACTIONr_bond_other_d0.0030.0221
X-RAY DIFFRACTIONr_angle_refined_deg1.5772.0264470
X-RAY DIFFRACTIONr_angle_other_deg1.211359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.715392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99123.141156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32915508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4961536
X-RAY DIFFRACTIONr_chiral_restr0.1020.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022517
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21640
X-RAY DIFFRACTIONr_nbd_other0.2570.242
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22229
X-RAY DIFFRACTIONr_nbtor_other0.1260.220
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8931.52045
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43923208
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.30231359
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2954.51260
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: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 69 -
Rwork0.197 1539 -
obs--78.17 %

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