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- PDB-8euk: cytochrome P450terp (cyp108A1) bound to ethylene glycol -

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Basic information

Entry
Database: PDB / ID: 8euk
Titlecytochrome P450terp (cyp108A1) bound to ethylene glycol
ComponentsCytochrome P450-terp
KeywordsOXIDOREDUCTASE / monooxygenase / complex / substrate / heme
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450-terp
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsGable, J.A. / Follmer, A.H. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131920 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Cooperative Substrate Binding Controls Catalysis in Bacterial Cytochrome P450terp (CYP108A1).
Authors: Gable, J.A. / Poulos, T.L. / Follmer, A.H.
History
DepositionOct 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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-terp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,51014
Polymers50,1491
Non-polymers1,36113
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.730, 68.730, 457.039
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Cytochrome P450-terp / Cytochrome P450terp / Cytochrome P450 108


Mass: 50148.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: cyp108, terPC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P33006, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.06 M magnesium chloride hexahyrate, 0.06 M calcium chloride dihydrate, 0.1 M sodium HEPES and MOPS (acid) pH 7.5, 20% v/v ethylene glycol, 10% v/v PEG 8000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→59.52 Å / Num. obs: 46098 / % possible obs: 99.92 % / Redundancy: 20.1 % / Biso Wilson estimate: 27.62 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.01765 / Net I/σ(I): 27.93
Reflection shellResolution: 1.984→2.055 Å / Mean I/σ(I) obs: 11.55 / Num. unique obs: 4465 / CC1/2: 0.995 / Rpim(I) all: 0.04957 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CPT

1cpt


Resolution: 1.98→59.52 Å / SU ML: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2064 2383 5.17 %
Rwork0.18 43697 -
obs0.1814 46080 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.07 Å2
Refinement stepCycle: LAST / Resolution: 1.98→59.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 91 281 3672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01123476
X-RAY DIFFRACTIONf_angle_d1.35024707
X-RAY DIFFRACTIONf_chiral_restr0.0812497
X-RAY DIFFRACTIONf_plane_restr0.0053614
X-RAY DIFFRACTIONf_dihedral_angle_d14.36591279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.020.2181230.19352535X-RAY DIFFRACTION99.96
2.02-2.070.211190.19112487X-RAY DIFFRACTION100
2.07-2.120.21951450.18882477X-RAY DIFFRACTION100
2.12-2.170.20611530.18382505X-RAY DIFFRACTION99.96
2.17-2.230.23131530.17692485X-RAY DIFFRACTION99.92
2.23-2.290.2141570.19052531X-RAY DIFFRACTION99.96
2.29-2.370.20791310.17492508X-RAY DIFFRACTION99.96
2.37-2.450.26351390.18852540X-RAY DIFFRACTION100
2.45-2.550.20541280.17542522X-RAY DIFFRACTION99.96
2.55-2.670.20081390.17752550X-RAY DIFFRACTION99.96
2.67-2.810.22721340.18592532X-RAY DIFFRACTION100
2.81-2.980.20631600.17732593X-RAY DIFFRACTION99.96
2.98-3.210.22661480.18632547X-RAY DIFFRACTION99.96
3.21-3.540.20371330.18392613X-RAY DIFFRACTION100
3.54-4.050.20021520.17132644X-RAY DIFFRACTION99.93
4.05-5.10.1821310.16422687X-RAY DIFFRACTION99.96
5.1-59.520.18771380.19082941X-RAY DIFFRACTION99.26

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