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- PDB-5hiw: Sorangium cellulosum So Ce56 cytochrome P450 260B1 -

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Basic information

Entry
Database: PDB / ID: 5hiw
TitleSorangium cellulosum So Ce56 cytochrome P450 260B1
ComponentsCytochrome P450 CYP260B1
KeywordsOXIDOREDUCTASE / P450 / CYTOCHROME / CYP / SORANGIUM / 260B1 / STEROIDS
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / 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 CYP260B1
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSalamanca-Pinzon, S.G. / Carius, Y. / Khatri, Y. / Bernhardt, R. / Lancaster, C.R.D.
CitationJournal: Febs Lett. / Year: 2016
Title: Structure-function analysis for the hydroxylation of Delta 4 C21-steroids by the myxobacterial CYP260B1.
Authors: Salamanca-Pinzon, S.G. / Khatri, Y. / Carius, Y. / Keller, L. / Muller, R. / Lancaster, C.R. / Bernhardt, R.
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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 CYP260B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2123
Polymers43,5711
Non-polymers6412
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-31 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.420, 60.420, 190.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

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Components

#1: Protein Cytochrome P450 CYP260B1


Mass: 43570.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (strain So ce56) (bacteria)
Description: HELMHOLTZ INSTITUTE OF PHARMACOLOGICAL SCIENCES (R. MUELLER)
Gene: cypA3, sce4806 / Plasmid: PCW / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: A9FFA1, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL HEXA-HISTIDINE TAG

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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: 2.13 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG 8000, ammonium sulfate, cacodylate / PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.85→35.3 Å / Num. obs: 35292 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.58 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.68
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.77 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.77 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VZ7

2vz7


Resolution: 1.85→35.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.998 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21876 1767 5 %RANDOM
Rwork0.17221 ---
obs0.17467 33523 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.084 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å2-0 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 44 244 3283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193196
X-RAY DIFFRACTIONr_bond_other_d0.0010.023121
X-RAY DIFFRACTIONr_angle_refined_deg21.9964367
X-RAY DIFFRACTIONr_angle_other_deg0.96337143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.74721.643140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2861541
X-RAY DIFFRACTIONr_chiral_restr0.1270.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213640
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02751
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_it2.8042.7631587
X-RAY DIFFRACTIONr_mcbond_other2.8042.7611586
X-RAY DIFFRACTIONr_mcangle_it3.7144.1331987
X-RAY DIFFRACTIONr_mcangle_other3.7164.1351988
X-RAY DIFFRACTIONr_scbond_it3.4393.1381609
X-RAY DIFFRACTIONr_scbond_other3.443.1391607
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1324.5462370
X-RAY DIFFRACTIONr_long_range_B_refined6.62122.4053882
X-RAY DIFFRACTIONr_long_range_B_other6.6222.4033883
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 103 -
Rwork0.192 2497 -
obs--100 %

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