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- PDB-8fib: Crystal Structure of Erwinia tracheiphila CYP114 -

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Basic information

Entry
Database: PDB / ID: 8fib
TitleCrystal Structure of Erwinia tracheiphila CYP114
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome P450 / 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 / Cytochrome P450
Similarity search - Component
Biological speciesErwinia tracheiphila PSU-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 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)49,4982
Polymers48,8811
Non-polymers6161
Water6,323351
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)92.931, 97.410, 107.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21A-618-

HOH

31A-857-

HOH

41A-890-

HOH

51A-949-

HOH

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Components

#1: Protein Cytochrome P450


Mass: 48881.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Erwinia tracheiphila PSU-1 (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.49 Å3/Da / Density % sol: 50.62 % / Mosaicity: 0.3 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5 / Details: 20-25% PEG3350, 0.1M Bis-Tris pH5.5

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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: Mar 10, 2017 / 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: 1.676→67.24 Å / Num. obs: 54653 / % possible obs: 97.4 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Net I/σ(I): 11.9
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
1.68-1.716.91.1961844326780.6470.4841.2931.594.4
9.03-67.246.80.04127934110.9940.0170.04541.799.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.85 Å57.02 Å
Translation1.85 Å57.02 Å

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
MOSFLM7.1.2data reduction
Aimless0.7.2data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z8O

1z8o


Resolution: 1.68→67.24 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 2616 4.79 %
Rwork0.1602 52018 -
obs0.1623 54634 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.1 Å2 / Biso mean: 32.7348 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 1.68→67.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 73 351 3680
Biso mean--18.71 37.1 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073479
X-RAY DIFFRACTIONf_angle_d0.9544746
X-RAY DIFFRACTIONf_dihedral_angle_d15.4442081
X-RAY DIFFRACTIONf_chiral_restr0.047523
X-RAY DIFFRACTIONf_plane_restr0.005621
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.68-1.70660.38221170.3058263894
1.7066-1.73940.351400.272265996
1.7394-1.77490.29961250.2416269896
1.7749-1.81350.24671290.2102269796
1.8135-1.85570.23571230.1965266796
1.8557-1.90210.21891380.182268997
1.9021-1.95350.25591380.1695270196
1.9535-2.0110.21371390.1634268697
2.011-2.07590.22711390.1568273497
2.0759-2.15010.18961400.1443273197
2.1501-2.23620.21441390.1335271197
2.2362-2.3380.18521400.1349273997
2.338-2.46130.19621410.138274898
2.4613-2.61550.1851410.1449273698
2.6155-2.81740.21071430.1515278598
2.8174-3.10090.19141430.1666278798
3.1009-3.54960.1961430.1574281299
3.5496-4.4720.19171460.1446284699
4.472-67.240.18351520.1645295499

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