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- PDB-5l91: The 2.2 A crystal structure of CYP109E1 from Bacillus megaterium ... -

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Basic information

Entry
Database: PDB / ID: 5l91
TitleThe 2.2 A crystal structure of CYP109E1 from Bacillus megaterium bound with four corticosterone molecules
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Bacillus / Bacterial Proteins / Binding Sites / Catalysis / Corticosterone / Cytochrome P-450 Enzyme System / Cytochrome P450 / Hydroxylation / Escherichia coli / Heme / Ligands / Molecular Structure / Oxidation-Reduction / Oxygen / Protein / Protein Structure / Secondary / Steroids / Substrate Specificity
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / 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
CORTICOSTERONE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJozwik, I.K. / Thunnissen, A.M.W.H.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission289217 Netherlands
CitationJournal: Febs J. / Year: 2016
Title: Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium.
Authors: Jozwik, I.K. / Kiss, F.M. / Abdulmughni, A. / Brill, E. / Zapp, J. / Pleiss, J. / Bernhardt, R. / Thunnissen, A.W.
History
DepositionJun 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Jan 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,64212
Polymers95,6372
Non-polymers4,00510
Water3,549197
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8216
Polymers47,8181
Non-polymers2,0025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8216
Polymers47,8181
Non-polymers2,0025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.418, 120.418, 140.803
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 18 and (name N or name...
21(chain B and (resseq 18:22 or (resid 23 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain A and ((resid 18 and (name N or name...AA1818
12GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
13GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
14GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
15GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
16GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
17GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
18GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
19GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
110GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
111GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
112GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
113GLNGLNHISHIS(chain A and ((resid 18 and (name N or name...AA17 - 40717 - 407
21THRTHRARGARG(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 2218 - 22
22PHEPHEPHEPHE(chain B and (resseq 18:22 or (resid 23 and (name...BB2323
23THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
24THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
25THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
26THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
27THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
28THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
29THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
210THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
211THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
212THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
213THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
214THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
215THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
216THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
217THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
218THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
219THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406
220THRTHRHISHIS(chain B and (resseq 18:22 or (resid 23 and (name...BB18 - 40618 - 406

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Components

#1: Protein Cytochrome P450


Mass: 47818.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (strain DSM 319) (bacteria)
Strain: DSM 319 / Gene: BMD_3874 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: D5DKI8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: D5DKI8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-C0R / CORTICOSTERONE / (11-BETA)-11,21-DIHYDROXY-PREGN-4-ENE-3,20-DIONE


Mass: 346.461 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.1 M Bis-Tris, pH 6.5 and 4% tacsimate reagent (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87261 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87261 Å / Relative weight: 1
ReflectionResolution: 2.2→48.9 Å / Num. obs: 60153 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.265.90.6691100
9.84-48.95.50.021197.8

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Processing

Software
NameVersionClassification
EDNAdata collection
XDSdata reduction
Aimless0.2.8data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L90

5l90


Resolution: 2.2→46.934 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 24.6
RfactorNum. reflection% reflection
Rfree0.2321 5833 5.05 %
Rwork0.1848 --
obs0.1872 60153 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.8 Å2 / Biso mean: 42.3849 Å2 / Biso min: 17.71 Å2
Refinement stepCycle: final / Resolution: 2.2→46.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6389 0 286 197 6872
Biso mean--50.61 35.09 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146872
X-RAY DIFFRACTIONf_angle_d1.3229379
X-RAY DIFFRACTIONf_chiral_restr0.0631018
X-RAY DIFFRACTIONf_plane_restr0.0081192
X-RAY DIFFRACTIONf_dihedral_angle_d12.8234133
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4656X-RAY DIFFRACTION5.247TORSIONAL
12B4656X-RAY DIFFRACTION5.247TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.22510.35931590.283836863845100
2.2251-2.25130.3151890.268836783867100
2.2513-2.27870.33781900.260336533843100
2.2787-2.30750.28042210.261336593880100
2.3075-2.33790.27961600.24537313891100
2.3379-2.36990.29852230.245136203843100
2.3699-2.40380.3011810.247637153896100
2.4038-2.43970.29811980.246735863784100
2.4397-2.47780.35291760.248636443820100
2.4778-2.51840.27752050.239736973902100
2.5184-2.56180.29221860.23436953881100
2.5618-2.60840.27571810.225236673848100
2.6084-2.65860.23292020.222136503852100
2.6586-2.71280.27182060.222936543860100
2.7128-2.77180.30261840.21436353819100
2.7718-2.83630.25111770.213836733850100
2.8363-2.90720.25432050.222136663871100
2.9072-2.98580.26542600.224835863846100
2.9858-3.07370.29842410.216136023843100
3.0737-3.17280.23941790.209237343913100
3.1728-3.28620.23611800.189236463826100
3.2862-3.41770.2341880.182436583846100
3.4177-3.57320.23032140.178436593873100
3.5732-3.76160.19091900.16336663856100
3.7616-3.99710.20652070.14763645385299
3.9971-4.30550.16411910.12923670386199
4.3055-4.73850.17171950.12583614380999
4.7385-5.42320.17151830.13373661384499
5.4232-6.82940.2091730.15913665383899
6.8294-46.9450.18361890.1483646383599

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