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- PDB-4fxb: Crystal structure of CYP105N1 from Streptomyces coelicolor: a cyt... -

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Basic information

Entry
Database: PDB / ID: 4fxb
TitleCrystal structure of CYP105N1 from Streptomyces coelicolor: a cytochrome P450 oxidase in the coelibactin siderophore biosynthetic pathway
ComponentsPutative cytochrome P450
KeywordsOXIDOREDUCTASE / P450 / CYP105N1 / Streptomyces coelicolor / coelibactin / estradiol
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, 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 / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHong, M.K. / Lim, Y.R. / Kim, J.K. / Kim, D.H. / Kang, L.W.
CitationJournal: Arch.Biochem.Biophys. / Year: 2012
Title: Crystal structure of cytochrome P450 CYP105N1 from Streptomyces coelicolor, an oxidase in the coelibactin siderophore biosynthetic pathway
Authors: Lim, Y.R. / Hong, M.K. / Kim, J.K. / Doan, T.T. / Kim, D.H. / Yun, C.H. / Chun, Y.J. / Kang, L.W. / Kim, D.
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative cytochrome P450
B: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2034
Polymers91,9702
Non-polymers1,2332
Water1,02757
1
A: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6012
Polymers45,9851
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6012
Polymers45,9851
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.086, 133.086, 227.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Putative cytochrome P450


Mass: 45984.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO7686 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EWP1
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M imidazole, 0.2M sodium chloride, 30%(w/v) PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 19, 2012
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 98528 / % possible obs: 88.8 % / Observed criterion σ(F): 18.3 / Observed criterion σ(I): 45
Reflection shellHighest resolution: 2.8 Å / % possible all: 88.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E5J

3e5j


Resolution: 2.9→19.93 Å / SU B: 18.015 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30235 1202 4.8 %RANDOM
Rwork0.28131 ---
all0.28238 23686 --
obs0.28238 23686 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.144 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 86 57 6021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0196082
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.4992.0028303
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.4115753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14522.222279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg28.68715973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8411580
X-RAY DIFFRACTIONr_chiral_restr0.1970.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0214666
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 246 -
Rwork0.381 4506 -
obs--89.53 %

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