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- PDB-8rtv: Crystal structure of CYP154E1 from Thermobifida fusca YX in compl... -

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Basic information

Entry
Database: PDB / ID: 8rtv
TitleCrystal structure of CYP154E1 from Thermobifida fusca YX in complex with 4-Phenylimidazole
ComponentsCytochrome P450-family protein
KeywordsOXIDOREDUCTASE / Cytochrome P450 / monooxygenase / alkene oxidation / allylic hydroxylation / heme protein / inhibitor / complex
Function / homology
Function and homology information


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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
4-PHENYL-1H-IMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450-family protein
Similarity search - Component
Biological speciesThermobifida fusca YX (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsBikbaev, K. / Hoelzel, S. / Urlacher, V. / Span, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031A223A Germany
CitationJournal: To Be Published
Title: Structural determination of the CYP154E1 cytochrome P450 from Thermobifida fusca YX
Authors: Bikbaev, K. / Hoelzel, S. / Urlacher, V. / Span, I.
History
DepositionJan 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450-family protein
B: Cytochrome P450-family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3166
Polymers87,7942
Non-polymers1,5214
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-73 kcal/mol
Surface area30360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.334, 97.176, 135.688
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 395 / Label seq-ID: 1 - 395

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Cytochrome P450-family protein


Mass: 43897.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca YX (bacteria) / Gene: Tfu_2976 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47KL3
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-231 / 4-PHENYL-1H-IMIDAZOLE


Mass: 144.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 20 % Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 29, 2021
RadiationMonochromator: Si-111 and Si-113 reflection / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2→48.984 Å / Num. obs: 56184 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.092 / Rrim(I) all: 0.242 / Χ2: 0.98 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 12.4 % / Rmerge(I) obs: 2.09 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4016 / CC1/2: 0.475 / Rpim(I) all: 0.882 / Rrim(I) all: 2.272 / Χ2: 0.79

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0425refinement
MOLREPphasing
Cootmodel building
XDSdata reduction
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.002→48.984 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.813 / SU ML: 0.158 / Cross valid method: NONE / ESU R: 0.219 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2714 2787 4.97 %
Rwork0.2184 53285 -
all0.221 --
obs-56072 99.618 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.445 Å2
Baniso -1Baniso -2Baniso -3
1-1.023 Å20 Å20 Å2
2---0.454 Å20 Å2
3----0.569 Å2
Refinement stepCycle: LAST / Resolution: 2.002→48.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6172 0 108 260 6540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126426
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166182
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.8658772
X-RAY DIFFRACTIONr_angle_other_deg0.5951.76614166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9825788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.3955.13972
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.034101046
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.21710290
X-RAY DIFFRACTIONr_chiral_restr0.0860.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027720
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021498
X-RAY DIFFRACTIONr_nbd_refined0.2210.21443
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.25887
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23171
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23311
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2258
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.216
X-RAY DIFFRACTIONr_nbd_other0.2380.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.24
X-RAY DIFFRACTIONr_mcbond_it3.1833.263158
X-RAY DIFFRACTIONr_mcbond_other3.1833.2613158
X-RAY DIFFRACTIONr_mcangle_it4.3745.8523944
X-RAY DIFFRACTIONr_mcangle_other4.3745.8533945
X-RAY DIFFRACTIONr_scbond_it3.823.5973268
X-RAY DIFFRACTIONr_scbond_other3.8193.5973269
X-RAY DIFFRACTIONr_scangle_it5.6166.4464828
X-RAY DIFFRACTIONr_scangle_other5.6166.4464829
X-RAY DIFFRACTIONr_lrange_it6.96831.8527211
X-RAY DIFFRACTIONr_lrange_other6.96531.8727179
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.0512474
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.114720.05007
12AX-RAY DIFFRACTIONLocal ncs0.114720.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.002-2.0540.3032180.30638040.30640830.9330.93498.5060.306
2.054-2.110.3252030.28638070.28840100.9240.9471000.282
2.11-2.1710.3171930.25837020.26138950.9230.9561000.252
2.171-2.2380.282010.24935730.25137820.9430.95899.78850.239
2.238-2.3110.3041900.23634930.2436890.9410.96299.83740.222
2.311-2.3920.3081770.22433360.22935310.9450.96899.49020.205
2.392-2.4820.31680.23132390.23434350.9390.96999.18490.209
2.482-2.5840.2631570.20831370.21132940.9610.9761000.184
2.584-2.6980.3051390.22930680.23232070.9420.9681000.202
2.698-2.8290.261570.21728820.2230420.9560.97299.90140.189
2.829-2.9820.2621530.21527360.21828910.9570.9799.93080.188
2.982-3.1620.2911260.2226140.22427410.940.96799.96350.197
3.162-3.3790.2741230.21324590.21625870.9550.97199.80670.195
3.379-3.6490.2341000.2123320.21124510.9650.97499.22480.197
3.649-3.9950.271110.19921180.20322340.9520.97799.77620.19
3.995-4.4620.2111020.17119370.17320480.9670.98199.56050.165
4.462-5.1460.209980.18217040.18318170.9760.98299.17450.177
5.146-6.2850.28720.21414660.21715540.9640.97798.97040.204
6.285-8.8160.257700.20811620.21112450.9610.97198.95580.206
8.816-48.9840.349290.2527160.2577460.9530.95899.8660.25

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