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- PDB-8fic: Crystal Structure of Erwinia tracheiphila CYP114 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8fic
TitleCrystal Structure of Erwinia tracheiphila CYP114 in complex with ent-kaurenoic acid (Crystal Form 1)
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / gibberellin
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-NE4 / Cytochrome P450
Similarity search - Component
Biological speciesErwinia tracheiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsStewart Jr., C.E. / Nagel, R.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131885 United States
German Research Foundation (DFG)NA 1261/1-2 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Dual factors required for cytochrome-P450-mediated hydrocarbon ring contraction in bacterial gibberellin phytohormone biosynthesis.
Authors: Nagel, R. / Alexander, L.E. / Stewart Jr., C.E. / Peters, R.J.
History
DepositionDec 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8003
Polymers48,8811
Non-polymers9192
Water4,846269
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)58.820, 70.460, 110.040
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

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Components

#1: Protein Cytochrome P450


Mass: 48881.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia tracheiphila (bacteria) / Gene: SY86_19565 / Plasmid: pET101 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Star / References: UniProt: A0A0M2KDV0
#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-NE4 / (8alpha,9beta,10alpha,13alpha)-kaur-16-en-18-oic acid / ent-kaurenoic acid


Mass: 302.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 47.27 % / Mosaicity: 0.32 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 16% PEG3350, 0.1M MES/Tris pH5.6, 0.2M Magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→70.46 Å / Num. obs: 51325 / % possible obs: 99.9 % / Redundancy: 7.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.048 / Rrim(I) all: 0.141 / Net I/σ(I): 7.5 / Num. measured all: 399178 / Scaling rejects: 142
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.738.11.082197427060.3930.3911.1511.999.9
8.98-70.467.70.10132164200.9930.0360.10716.899.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å59.34 Å
Translation2 Å59.34 Å

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
MOSFLMdata reduction
Aimless0.7.1data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RLP

7rlp
PDB Unreleased entry


Resolution: 1.7→59.34 Å / SU ML: 0.2119 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6455
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 2000 3.9 %
Rwork0.1597 49248 -
obs0.1609 51248 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 0 269 3598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383501
X-RAY DIFFRACTIONf_angle_d0.7924790
X-RAY DIFFRACTIONf_chiral_restr0.0411527
X-RAY DIFFRACTIONf_plane_restr0.0038626
X-RAY DIFFRACTIONf_dihedral_angle_d17.99411285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.31021400.26173469X-RAY DIFFRACTION99.89
1.74-1.790.32741410.24513451X-RAY DIFFRACTION99.78
1.79-1.840.30811410.22123479X-RAY DIFFRACTION99.86
1.84-1.90.25541420.19813475X-RAY DIFFRACTION99.86
1.9-1.970.24811410.18073483X-RAY DIFFRACTION99.86
1.97-2.050.2061420.16213506X-RAY DIFFRACTION99.92
2.05-2.140.20021410.15943462X-RAY DIFFRACTION99.78
2.14-2.250.21331420.14363500X-RAY DIFFRACTION99.84
2.25-2.390.1871410.14083484X-RAY DIFFRACTION99.83
2.39-2.580.21351440.14573514X-RAY DIFFRACTION99.89
2.58-2.840.21411430.14973535X-RAY DIFFRACTION99.97
2.84-3.250.18781440.15693571X-RAY DIFFRACTION99.87
3.25-4.090.16161460.15023579X-RAY DIFFRACTION99.92
4.09-59.340.14931520.15873740X-RAY DIFFRACTION99.57

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