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- PDB-2jjn: Structure of closed cytochrome P450 EryK -

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Basic information

Entry
Database: PDB / ID: 2jjn
TitleStructure of closed cytochrome P450 EryK
ComponentsCYTOCHROME P450 113A1
KeywordsOXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING / ANTIBIOTIC BIOSYNTHESIS / TIE-ROD MECHANISM OF ACTION / CYTOCHROME P450 / 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 / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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
PROTOPORPHYRIN IX CONTAINING FE / Erythromycin C-12 hydroxylase
Similarity search - Component
Biological speciesSACCHAROPOLYSPORA ERYTHRAEA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 1.1Jul 13, 2011Group: Advisory / 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)46,4447
Polymers45,3471
Non-polymers1,0976
Water9,926551
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.460, 68.004, 57.407
Angle α, β, γ (deg.)90.00, 101.05, 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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 1 TO LEU ENGINEERED RESIDUE IN CHAIN A, PHE 330 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: 1.9 Å3/Da / Density % sol: 34.9 %
Crystal growpH: 6.5 / Details: 2.0M AMMONIUM SULPHATE, 0.1M BIS-TRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 53926 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 16.06 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 19.1 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VRU

2vru
PDB Unreleased entry


Resolution: 1.59→56.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.803 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COORDINATES START FROM A.A. 17 BECAUSE THERE WAS NOT ELECTRON DENSITY FOR PREVIOUS RESIDUES
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2725 5.1 %RANDOM
Rwork0.16 ---
obs0.162 50735 98.8 %-
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: 23.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.01 Å2
2--1.47 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.59→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 68 551 3669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223365
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6362.0144597
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32823.353170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31115576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1381538
X-RAY DIFFRACTIONr_chiral_restr0.1090.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.21841
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22323
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2480
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.2123
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.277
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2221.52031
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.94323273
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.54731473
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7554.51322
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: 1.59→1.63 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.227 202
Rwork0.179 3455
Refinement TLS params.Method: refined / Origin x: 21.479 Å / Origin y: -0.271 Å / Origin z: 9.34 Å
111213212223313233
T-0.12 Å20.0083 Å2-0.01 Å2--0.121 Å20.0105 Å2---0.0723 Å2
L0.4976 °20.0212 °2-0.0854 °2-0.0954 °20.0354 °2--0.3685 °2
S-0.0057 Å °-0.0115 Å °0.0532 Å °-0.0004 Å °-0.0082 Å °-0.0389 Å °-0.0252 Å °0.0511 Å °0.0139 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 40
2X-RAY DIFFRACTION1A56 - 64
3X-RAY DIFFRACTION1A93 - 105
4X-RAY DIFFRACTION1A108 - 113
5X-RAY DIFFRACTION1A115 - 128
6X-RAY DIFFRACTION1A135 - 141
7X-RAY DIFFRACTION1A143 - 152
8X-RAY DIFFRACTION1A160 - 171
9X-RAY DIFFRACTION1A180 - 191
10X-RAY DIFFRACTION1A192 - 206
11X-RAY DIFFRACTION1A212 - 218
12X-RAY DIFFRACTION1A228 - 259
13X-RAY DIFFRACTION1A261 - 269
14X-RAY DIFFRACTION1A274 - 284
15X-RAY DIFFRACTION1A316 - 320
16X-RAY DIFFRACTION1A356 - 373

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