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- PDB-8gtl: Crystal Structure of Cytochrome P450 (CYP101D5) -

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Basic information

Entry
Database: PDB / ID: 8gtl
TitleCrystal Structure of Cytochrome P450 (CYP101D5)
Componentscytochrome P450 CYP101D5
KeywordsTRANSFERASE / ionone / cytochrome P450 / chemical modification / heme oxidation
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesSphingomonas echinoides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDo, H. / Lee, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Korea)NRF-2019R1D1A3A03103903 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2022
Title: Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides.
Authors: Subedi, P. / Do, H. / Lee, J.H. / Oh, T.J.
History
DepositionSep 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytochrome P450 CYP101D5
B: cytochrome P450 CYP101D5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9384
Polymers91,7052
Non-polymers1,2332
Water23413
1
A: cytochrome P450 CYP101D5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4692
Polymers45,8521
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cytochrome P450 CYP101D5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4692
Polymers45,8521
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.524, 109.573, 113.878
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 9 through 43 or resid 46...
d_2ens_1(chain "B" and (resid 9 through 185 or resid 188 through 216 or resid 221 through 409))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRGLNA1 - 35
d_12ens_1ASPALAA38 - 80
d_13ens_1GLUGLYA83 - 206
d_14ens_1ASPASPA208
d_15ens_1ILETRPA210 - 397
d_21ens_1THRGLUB1 - 173
d_22ens_1THRGLYB176 - 204
d_23ens_1ASPTRPB206 - 394

NCS oper: (Code: givenMatrix: (-0.971742103419, -0.159033955719, -0.174429026745), (-0.171515887997, 0.983419694168, 0.0588897723513), (0.162171466687, 0.0871430206691, -0.982907172291)Vector: -25. ...NCS oper: (Code: given
Matrix: (-0.971742103419, -0.159033955719, -0.174429026745), (-0.171515887997, 0.983419694168, 0.0588897723513), (0.162171466687, 0.0871430206691, -0.982907172291)
Vector: -25.5903684593, 7.30399247457, -55.5054618165)

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Components

#1: Protein cytochrome P450 CYP101D5


Mass: 45852.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas echinoides (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 293 K / Method: liquid diffusion / Details: 1.6 M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→43.79 Å / Num. obs: 14555 / % possible obs: 99.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 92.37 Å2 / CC1/2: 1 / Net I/σ(I): 10.1
Reflection shellResolution: 3.2→3.31 Å / Num. unique obs: 1195 / CC1/2: 0.529

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Processing

Software
NameVersionClassification
Blu-Ice1.20.1_4487data collection
PHENIX1.20.1_4487refinement
Blu-Ice1.20.1_4487data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NV5

3nv5


Resolution: 3.2→43.79 Å / SU ML: 0.6047 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.1037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.319 1443 9.95 %
Rwork0.2624 13064 -
obs0.268 14507 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.19 Å2
Refinement stepCycle: LAST / Resolution: 3.2→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6254 0 86 13 6353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236509
X-RAY DIFFRACTIONf_angle_d0.54788866
X-RAY DIFFRACTIONf_chiral_restr0.0429948
X-RAY DIFFRACTIONf_plane_restr0.00451162
X-RAY DIFFRACTIONf_dihedral_angle_d11.95462430
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.72676268356 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.320.44671360.3691195X-RAY DIFFRACTION92.05
3.32-3.450.37971380.32761295X-RAY DIFFRACTION99.51
3.45-3.610.35751460.32811296X-RAY DIFFRACTION99.86
3.61-3.80.37161470.30531287X-RAY DIFFRACTION99.72
3.8-4.030.33571380.26931305X-RAY DIFFRACTION99.79
4.04-4.350.32791430.2531302X-RAY DIFFRACTION99.86
4.35-4.780.25761490.23351323X-RAY DIFFRACTION99.93
4.78-5.470.32011450.23991307X-RAY DIFFRACTION99.79
5.47-6.890.33471530.27091351X-RAY DIFFRACTION100
6.9-43.790.27461480.22881403X-RAY DIFFRACTION98.79
Refinement TLS params.Method: refined / Origin x: -14.0889664131 Å / Origin y: 26.4089312208 Å / Origin z: -28.9711694004 Å
111213212223313233
T0.869720961475 Å20.0203353687987 Å2-0.0475038448102 Å2-0.556712934755 Å2-0.00707607865011 Å2--0.574349015637 Å2
L0.549818640423 °20.0615265613357 °2-0.978936163831 °2-0.158546419584 °2-0.219871492148 °2--2.29547718389 °2
S0.027089742302 Å °-0.00961270893033 Å °-0.0654129923525 Å °0.0827974056737 Å °-0.011946586894 Å °-0.0406471781399 Å °-0.0441872925127 Å °-0.020626683662 Å °-0.0260341482535 Å °
Refinement TLS groupSelection details: all

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