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- PDB-5l92: The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium ... -

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Basic information

Entry
Database: PDB / ID: 5l92
TitleThe 2.1 A crystal structure of CYP109E1 from Bacillus megaterium in complex with corticosterone
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 / MALONIC ACID / Cytochrome P450
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / pdbx_initial_refinement_model / struct_conn
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

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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)97,3206
Polymers95,6372
Non-polymers1,6834
Water2,216123
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8864
Polymers47,8181
Non-polymers1,0673
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)60.495, 135.701, 61.567
Angle α, β, γ (deg.)90.000, 114.420, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 1 / Source method: obtained synthetically / Formula: C21H30O4
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 9% PEG 3350 and 8% tacsimate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.1→47.98 Å / Num. obs: 51292 / % possible obs: 97.4 % / Redundancy: 3 % / Biso Wilson estimate: 30.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.022 / Rrim(I) all: 0.04 / Net I/σ(I): 23.3 / Num. measured all: 156293
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.162.90.261198.8
8.91-47.983.30.013196.1

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Processing

Software
NameVersionClassification
EDNAdata collection
XDSdata reduction
Aimless0.5.1data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GGV

4ggv


Resolution: 2.1→42.766 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 24.88
RfactorNum. reflection% reflection
Rfree0.2431 5216 5.19 %
Rwork0.2009 --
obs0.203 51292 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.73 Å2 / Biso mean: 38.5779 Å2 / Biso min: 19.81 Å2
Refinement stepCycle: final / Resolution: 2.1→42.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6192 0 118 123 6433
Biso mean--29.67 32.27 -
Num. residues----756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146460
X-RAY DIFFRACTIONf_angle_d1.2998760
X-RAY DIFFRACTIONf_chiral_restr0.071942
X-RAY DIFFRACTIONf_plane_restr0.0071124
X-RAY DIFFRACTIONf_dihedral_angle_d16.372467
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 (%)
2.1-2.12390.30232270.26533215344298
2.1239-2.14890.2822190.28113189340899
2.1489-2.17510.30961900.26613197338799
2.1751-2.20260.34122070.26353270347799
2.2026-2.23160.34141810.31423051323294
2.2316-2.26210.54631240.44132194231866
2.2621-2.29450.31121960.29273038323494
2.2945-2.32870.26642000.24043254345499
2.3287-2.36510.26991700.2253252342299
2.3651-2.40390.28351560.2323246340299
2.4039-2.44530.25131740.22623260343499
2.4453-2.48980.25361720.23163233340598
2.4898-2.53760.29791650.23273295346099
2.5376-2.58940.24991550.22333257341299
2.5894-2.64570.26091860.22283254344098
2.6457-2.70730.26181730.22243222339598
2.7073-2.7750.28691970.2233204340198
2.775-2.850.30011930.23653247344099
2.85-2.93380.27391910.221232443435100
2.9338-3.02850.30811960.230532993495100
3.0285-3.13670.27262310.22483174340599
3.1367-3.26220.28181420.20793261340399
3.2622-3.41070.25611440.20823302344699
3.4107-3.59040.23881640.20193201336597
3.5904-3.81520.18751620.19213000316291
3.8152-4.10960.20361240.15843183330795
4.1096-4.52270.15571120.14243244335698
4.5227-5.17620.15291690.14043215338497
5.1762-6.51780.19721850.16333182336797
6.5178-42.77460.17141110.14483192330396

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