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- PDB-9x0n: Crystal structure of a self-sufficient cytochrome P450 from Shima... -

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Basic information

Entry
Database: PDB / ID: 9x0n
TitleCrystal structure of a self-sufficient cytochrome P450 from Shimazuella soli.
ComponentsSoP450
KeywordsOXIDOREDUCTASE / cytochrome P450 / self-sufficient / Heme
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesShimazuella soli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsLiu, Z.W. / Huang, J.-W. / Wang, T. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of a self-sufficient cytochrome P450 from Shimazuella soli.
Authors: Liu, Z.W. / Huang, J.-W. / Wang, T. / Chen, C.-C. / Guo, R.-T.
History
DepositionSep 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SoP450
B: SoP450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,7938
Polymers242,0762
Non-polymers3,7176
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18300 Å2
ΔGint-97 kcal/mol
Surface area77880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.559, 205.559, 83.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein SoP450


Mass: 121038.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shimazuella soli (bacteria) / Production host: Escherichia coli (E. coli)
#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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 4.21 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5; 13% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97621 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97621 Å / Relative weight: 1
ReflectionResolution: 3.38→25 Å / Num. obs: 54693 / % possible obs: 99.2 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 26.5
Reflection shellResolution: 3.38→3.5 Å / Num. unique obs: 5456 / CC1/2: 0.701

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SAINTdata scaling
PDB_EXTRACTdata extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.38→24.69 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 1960 3.95 %RANDOM
Rwork0.1931 ---
obs0.1952 49600 89.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.38→24.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16268 0 254 60 16582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116889
X-RAY DIFFRACTIONf_angle_d1.40322902
X-RAY DIFFRACTIONf_dihedral_angle_d10.2712264
X-RAY DIFFRACTIONf_chiral_restr0.0672449
X-RAY DIFFRACTIONf_plane_restr0.0112962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.38-3.470.3779530.29471198X-RAY DIFFRACTION32
3.47-3.560.3781730.27572007X-RAY DIFFRACTION53
3.56-3.660.32231230.26563245X-RAY DIFFRACTION85
3.66-3.780.30241640.2383731X-RAY DIFFRACTION98
3.78-3.920.29931470.23853719X-RAY DIFFRACTION99
3.92-4.070.25161640.21693753X-RAY DIFFRACTION99
4.07-4.260.28481590.20213747X-RAY DIFFRACTION99
4.26-4.480.22261530.18463749X-RAY DIFFRACTION99
4.48-4.760.22961580.17583750X-RAY DIFFRACTION99
4.76-5.120.21281600.17563771X-RAY DIFFRACTION100
5.12-5.630.26121490.18793756X-RAY DIFFRACTION99
5.64-6.440.2751480.19393756X-RAY DIFFRACTION99
6.44-8.060.22111490.15963725X-RAY DIFFRACTION99
8.07-24.690.14691600.11863733X-RAY DIFFRACTION99

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