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- PDB-5l90: The crystal structure of substrate-free CYP109E1 from Bacillus me... -

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Basic information

Entry
Database: PDB / ID: 5l90
TitleThe crystal structure of substrate-free CYP109E1 from Bacillus megaterium at 2.55 Angstrom resolution
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Bacillus / Bacterial Proteins / Binding Sites / Catalysis / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 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 / 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

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Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8704
Polymers95,6372
Non-polymers1,2332
Water1448
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4352
Polymers47,8181
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4352
Polymers47,8181
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.288, 121.288, 144.161
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 21 and (name O or name...
21(chain B and ((resid 21 and (name N or name...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLU(chain A and ((resid 21 and (name O or name...AA2121
12HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
13HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
14HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
15HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
16HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
17HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
18HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
19HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
110HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
111HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
112HISHIS(chain A and ((resid 21 and (name O or name...AA21 - 40521 - 405
21GLUGLU(chain B and ((resid 21 and (name N or name...BB2121
22HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
23HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
24HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
25HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
26HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
27HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
28HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
29HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
210HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
211HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405
212HISHIS(chain B and ((resid 21 and (name N or name...BB21 - 40521 - 405

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
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: ID29 / Wavelength: 1.04541 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04541 Å / Relative weight: 1
ReflectionResolution: 2.55→60.64 Å / Num. obs: 40454 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 50.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Net I/σ(I): 11.6 / Num. measured all: 293843 / Scaling rejects: 52
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.55-2.656.90.802199.9
9.19-60.646.90.045199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å60.64 Å
Translation2.7 Å60.64 Å

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Processing

Software
NameVersionClassification
EDNAdata collection
iMOSFLMdata reduction
Aimless0.2.8data scaling
PHASERphasing
PHENIX2.5.5model building
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ggv

4ggv


Resolution: 2.55→60.64 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 32.16
RfactorNum. reflection% reflection
Rfree0.2588 3872 5.02 %
Rwork0.2144 --
obs0.2166 40454 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 209.25 Å2 / Biso mean: 67.1434 Å2 / Biso min: 23.94 Å2
Refinement stepCycle: final / Resolution: 2.55→60.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 86 8 6394
Biso mean--44.45 41.29 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176542
X-RAY DIFFRACTIONf_angle_d1.6798876
X-RAY DIFFRACTIONf_chiral_restr0.074948
X-RAY DIFFRACTIONf_plane_restr0.0161148
X-RAY DIFFRACTIONf_dihedral_angle_d16.8492502
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4665X-RAY DIFFRACTION7.615TORSIONAL
12B4665X-RAY DIFFRACTION7.615TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.58110.46161360.370726072743100
2.5811-2.61380.41051360.35362614275099
2.6138-2.64820.39231550.343426122767100
2.6482-2.68450.38161260.333526342760100
2.6845-2.72280.40511050.318726342739100
2.7228-2.76350.36761530.312726322785100
2.7635-2.80660.33841220.302725942716100
2.8066-2.85270.32941310.294526012732100
2.8527-2.90180.35891420.289526392781100
2.9018-2.95460.3831300.287126632793100
2.9546-3.01140.32951690.29625772746100
3.0114-3.07290.35041170.279926272744100
3.0729-3.13970.34341450.289726182763100
3.1397-3.21280.29881400.277125982738100
3.2128-3.29310.29521380.262226482786100
3.2931-3.38210.33281520.253626162768100
3.3821-3.48160.23141090.248926442753100
3.4816-3.5940.28981140.239926312745100
3.594-3.72240.27931450.2225912736100
3.7224-3.87150.21931250.207526652790100
3.8715-4.04760.29331620.193526112773100
4.0476-4.2610.20421680.180425572725100
4.261-4.52780.25971400.157226362776100
4.5278-4.87730.19491290.156726382767100
4.8773-5.36790.15741600.156825982758100
5.3679-6.1440.21481750.174625852760100
6.144-7.73820.18231350.17282609274499
7.7382-60.66110.19291130.144126522765100

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