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- PDB-7snm: Lanosterol-bound P450 domain of the CYP51-ferredoxin fusion prote... -

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Basic information

Entry
Database: PDB / ID: 7snm
TitleLanosterol-bound P450 domain of the CYP51-ferredoxin fusion protein from Methylococcus capsulatus
ComponentsCytochrome P450 51
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 FOLD / CYP51 / HEME / STEROL BIOSYNTHESIS
Function / homology
Function and homology information


sterol 14alpha-demethylase / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / bile acid biosynthetic process / cholesterol homeostasis / iron ion binding / heme binding
Similarity search - Function
4Fe-4S single cluster domain / Cytochrome P450, E-class, group IV / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / LANOSTEROL / Cytochrome P450 51
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLepesheva, G.I. / Hargrove, T. / Wawrzak, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01067871 United States
CitationJournal: Sci Rep / Year: 2022
Title: Unravelling the role of transient redox partner complexes in P450 electron transfer mechanics.
Authors: Hargrove, T.Y. / Lamb, D.C. / Smith, J.A. / Wawrzak, Z. / Kelly, S.L. / Lepesheva, G.I.
History
DepositionOct 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Assembly

Deposited unit
A: Cytochrome P450 51
B: Cytochrome P450 51
C: Cytochrome P450 51
D: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,10812
Polymers249,9354
Non-polymers4,1738
Water6,143341
1
A: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5273
Polymers62,4841
Non-polymers1,0432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5273
Polymers62,4841
Non-polymers1,0432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5273
Polymers62,4841
Non-polymers1,0432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5273
Polymers62,4841
Non-polymers1,0432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.210, 206.160, 81.430
Angle α, β, γ (deg.)90.000, 114.090, 90.000
Int Tables number4
Space group name H-MP1211
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 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 6 - 448 / Label seq-ID: 6 - 448

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cytochrome P450 51 /


Mass: 62483.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: cyp51, MCA2711 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS-164 / References: UniProt: Q603T8, sterol 14alpha-demethylase
#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-LAN / LANOSTEROL / Lanosterol


Mass: 426.717 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H50O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.1
Details: Na-citrate tribasic dehydrate, PEG 8,000, dodecyltrimethylammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 10, 2021 / Details: Focussing mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→74.45 Å / Num. obs: 67008 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.4
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4997 / CC1/2: 0.96 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6mi0

6mi0


Resolution: 2.55→74.45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.883 / SU B: 30.255 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 3792 5.4 %RANDOM
Rwork0.2045 ---
obs0.2073 67008 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 289.91 Å2 / Biso mean: 54.83 Å2 / Biso min: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0 Å2-0.24 Å2
2--0.37 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 2.55→74.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14130 0 296 341 14767
Biso mean--25.87 47.06 -
Num. residues----1765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01314795
X-RAY DIFFRACTIONr_bond_other_d0.0090.01514170
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.67320115
X-RAY DIFFRACTIONr_angle_other_deg1.4211.58332498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67751759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.79220.282851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.175152504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.56615150
X-RAY DIFFRACTIONr_chiral_restr0.0640.21873
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0216544
X-RAY DIFFRACTIONr_gen_planes_other0.0160.023552
X-RAY DIFFRACTIONr_rigid_bond_restr6.01328965
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A143750.1
12B143750.1
21A141710.11
22C141710.11
31A137500.12
32D137500.12
41B140460.12
42C140460.12
51B137310.13
52D137310.13
61C136200.13
62D136200.13
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 272 -
Rwork0.359 4997 -
all-5269 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.51420.1899-0.12970.30920.14090.2254-0.16140.06460.02410.01320.1110.01760.04820.06290.05040.1855-0.06410.00160.1094-0.03660.1580.2336.916825.8138
20.2213-0.0564-0.030.39910.05780.45950.0139-0.09260.1761-0.04070.0867-0.12160.1045-0.1606-0.10070.1174-0.0020.00940.1569-0.05340.16830.046515.6136-18.532
30.30020.483-0.0650.8045-0.1930.3251-0.03350.11210.1344-0.05060.16060.25570.04990.0409-0.12710.1397-0.0380.00810.09110.09660.3229-32.328567.50624.7888
40.6825-0.39840.25570.6306-0.30150.29550.118-0.04850.0022-0.3267-0.11670.12030.2229-0.0014-0.00130.42930.0376-0.01410.0662-0.06030.0603-31.0791-11.69520.2116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 602
2X-RAY DIFFRACTION2B6 - 602
3X-RAY DIFFRACTION3C6 - 602
4X-RAY DIFFRACTION4D6 - 602

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