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- PDB-5liv: Crystal structure of myxobacterial CYP260A1 -

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Basic information

Entry
Database: PDB / ID: 5liv
TitleCrystal structure of myxobacterial CYP260A1
ComponentsCytochrome P450 CYP260A1,Cytochrome P450 CYP260A1
KeywordsOXIDOREDUCTASE / 1-alpha-hydroxylase / steroid / Sorangium cellulosum / redox pool
Function / homology
Function and homology information


C-19 steroid 1alpha-hydroxylase / 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 / C-19 steroid 1alpha-hydroxylase
Similarity search - Component
Biological speciesSorangium cellulosum So ce56 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsCarius, Y. / Khatri, Y. / Bernhardt, R. / Lancaster, C.R.D.
Citation
Journal: FEBS Lett. / Year: 2016
Title: Structural characterization of CYP260A1 from Sorangium cellulosum to investigate the 1 alpha-hydroxylation of a mineralocorticoid.
Authors: Khatri, Y. / Carius, Y. / Ringle, M. / Lancaster, C.R. / Bernhardt, R.
#1: Journal: Chembiochem / Year: 2016
Title: Substrate Hunting for the Myxobacterial CYP260A1 Revealed New 1alpha-Hydroxylated Products from C-19 Steroids.
Authors: Khatri, Y. / Ringle, M. / Lisurek, M. / von Kries, J.P. / Zapp, J. / Bernhardt, R.
History
DepositionJul 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1
B: Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1
C: Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1
D: Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,04343
Polymers199,2674
Non-polymers5,77639
Water6,071337
1
A: Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,45912
Polymers49,8171
Non-polymers1,64211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9888
Polymers49,8171
Non-polymers1,1717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,17210
Polymers49,8171
Non-polymers1,3559
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,42413
Polymers49,8171
Non-polymers1,60712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)234.560, 234.560, 96.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-510-

SO4

21A-678-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA51 - 44651 - 446
21METMETBB51 - 44651 - 446
12ASPASPAA52 - 44552 - 445
22ASPASPCC52 - 44552 - 445
13ASPASPAA52 - 44652 - 446
23ASPASPDD52 - 44652 - 446
14PHEPHEBB53 - 44553 - 445
24PHEPHECC53 - 44553 - 445
15ASPASPBB52 - 44652 - 446
25ASPASPDD52 - 44652 - 446
16ASPASPCC52 - 44552 - 445
26ASPASPDD52 - 44552 - 445

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1


Mass: 49816.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum So ce56 (bacteria)
Gene: sce1588 / Production host: Escherichia coli (E. coli)
References: UniProt: A9FDB7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 6 types, 376 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 MES monohydrate, pH 6.5, with 1.6 M magnesium sulphate heptahydrate

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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: 2.67→69.93 Å / Num. obs: 86158 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.121 / Net I/σ(I): 4.8
Reflection shellResolution: 2.67→2.72 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLM7.1.1data reduction
Aimless0.3.11data scaling
MOLREP11.02.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HIW

5hiw


Resolution: 2.67→69.93 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.064 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 4262 4.9 %RANDOM
Rwork0.18731 ---
obs0.1891 81873 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.24 Å20 Å2
2---0.47 Å2-0 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.67→69.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12130 0 359 337 12826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01912799
X-RAY DIFFRACTIONr_bond_other_d0.0090.0212301
X-RAY DIFFRACTIONr_angle_refined_deg1.92217401
X-RAY DIFFRACTIONr_angle_other_deg1.583328096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57551571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75321.951569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.158152013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.60715147
X-RAY DIFFRACTIONr_chiral_restr0.10.21933
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02114394
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023025
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_it3.8954.086293
X-RAY DIFFRACTIONr_mcbond_other3.894.086292
X-RAY DIFFRACTIONr_mcangle_it5.9766.1087858
X-RAY DIFFRACTIONr_mcangle_other5.9766.1097859
X-RAY DIFFRACTIONr_scbond_it4.9834.6676506
X-RAY DIFFRACTIONr_scbond_other4.9074.6486474
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6126.729495
X-RAY DIFFRACTIONr_long_range_B_refined9.88232.57114726
X-RAY DIFFRACTIONr_long_range_B_other9.88232.57114727
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A208540.16
12B208540.16
21A226020.14
22C226020.14
31A220930.15
32D220930.15
41B208230.17
42C208230.17
51B209030.16
52D209030.16
61C217130.15
62D217130.15
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 306 -
Rwork0.295 5894 -
obs--98.01 %

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