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- PDB-6ro8: The crystal structure of Acinetobacter radioresistens CYP116B5 he... -

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Basic information

Entry
Database: PDB / ID: 6ro8
TitleThe crystal structure of Acinetobacter radioresistens CYP116B5 heme domain
ComponentsCytochrome P450 RhF
KeywordsOXIDOREDUCTASE / cytochrome P450 / monooxygenases / biocatalysis
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding / heme binding
Similarity search - Function
2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / FAD-binding domain, ferredoxin reductase-type ...2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HISTIDINE / Cytochrome P450 RhF
Similarity search - Component
Biological speciesAcinetobacter radioresistens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCiaramella, A. / Catucci, G. / Gilardi, G. / Di Nardo, G.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Crystal structure of bacterial CYP116B5 heme domain: New insights on class VII P450s structural flexibility and peroxygenase activity.
Authors: Ciaramella, A. / Catucci, G. / Gilardi, G. / Di Nardo, G.
History
DepositionMay 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 RhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6693
Polymers51,8961
Non-polymers7732
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-23 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.9, 109.9, 164.2
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Cytochrome P450 RhF


Mass: 51896.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter radioresistens (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: G9BWN9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.19 Å3/Da / Density % sol: 76.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM amino acids (0.02 M DL-Arginine hydrochloride, 0.02M DL-Threonine, 0.02M DL-Histidine monohydrochloride monohydrate, 0.02M DL-5-Hydroxylysine hydrochloride, 0.02M trans-4-hydroxy-L- ...Details: 100 mM amino acids (0.02 M DL-Arginine hydrochloride, 0.02M DL-Threonine, 0.02M DL-Histidine monohydrochloride monohydrate, 0.02M DL-5-Hydroxylysine hydrochloride, 0.02M trans-4-hydroxy-L-proline), 0.1 M Gly-Gly, AMPD buffer pH 8.5, 50% v/v of 25% w/v PEG 4000, 40% w/v 1,2,6- Hexanetriol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→109.9 Å / Num. obs: 31654 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 73.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Net I/av σ(I): 19.9 / Net I/σ(I): 19.9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3788 / CC1/2: 0.584 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
Cootmodel building
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GII

6gii


Resolution: 2.6→91.33 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24 --RANDOM
Rwork0.2 ---
obs-30052 100 %-
Displacement parametersBiso max: 202.59 Å2 / Biso mean: 88.6208 Å2 / Biso min: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.6→91.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 54 71 3479

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