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

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Basic information

Entry
Database: PDB / ID: 8fid
TitleCrystal Structure of Erwinia tracheiphila CYP114 in complex with ent-kaurenoic acid (Crystal Form 2)
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / gibberellin
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-NE4 / Cytochrome P450
Similarity search - Component
Biological speciesErwinia tracheiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 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
Water4,594255
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)106.460, 70.030, 59.280
Angle α, β, γ (deg.)90.000, 95.250, 90.000
Int Tables number5
Space group name H-MC121

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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 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.25 Å3/Da / Density % sol: 45.35 % / Mosaicity: 0.36 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 25% PEG4000, 0.1M MES/Tris pH5.6, 0.15M Ammonium sulfate, 10mM Cadmium chloride hydrate

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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→59.031 Å / Num. obs: 47323 / % possible obs: 98.6 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.071 / Rrim(I) all: 0.148 / Net I/σ(I): 5
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
1.7-1.7341.1221015925260.1060.6141.2851.398.9
8.98-59.034.40.05815093440.9940.030.06520.199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.7 Å59.03 Å
Translation1.7 Å59.03 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2data reduction
Aimless0.6.2data scaling
PHASER2.8.0phasing
PHENIX1.14refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RLP

7rlp
PDB Unreleased entry


Resolution: 1.83→59.031 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1593 4.22 %
Rwork0.1876 36123 -
obs0.1892 37716 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.62 Å2 / Biso mean: 40.8251 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 1.83→59.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 124 255 3607
Biso mean--25.01 42.89 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.83-1.88910.40041410.3513323898
1.8891-1.95660.3041450.3018325698
1.9566-2.0350.31851450.2604330199
2.035-2.12760.311460.2246328298
2.1276-2.23980.22041410.1936323998
2.2398-2.38010.21341440.1787325798
2.3801-2.56390.22511460.1797330099
2.5639-2.82190.221450.1656329399
2.8219-3.23020.2241450.1774328398
3.2302-4.06960.21131460.1608330698
4.0696-59.0310.19311490.175336898

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