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- PDB-7ccf: Mechanism insights on steroselective oxidation of phosphorylated ... -

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Basic information

Entry
Database: PDB / ID: 7ccf
TitleMechanism insights on steroselective oxidation of phosphorylated ethylphenols with cytochrome P450 CreJ
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 monooxygenase
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
(3-ethylphenyl) dihydrogen phosphate / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDong, S. / Du, L. / Li, S.Y. / Feng, Y.G.
Citation
Journal: Appl.Environ.Microbiol. / Year: 2021
Title: Structural Basis for Selective Oxidation of Phosphorylated Ethylphenols by Cytochrome P450 Monooxygenase CreJ.
Authors: Dong, S. / Chen, J. / Zhang, X. / Guo, F. / Ma, L. / You, C. / Wang, X. / Zhang, W. / Wan, X. / Liu, S.J. / Yao, L.S. / Li, S. / Du, L. / Feng, Y.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2017
Title: Selective oxidation of aliphatic C-H bonds in alkylphenols by a chemomimetic biocatalytic system.
Authors: Du, L. / Dong, S. / Zhang, X. / Jiang, C. / Chen, J. / Yao, L. / Wang, X. / Wan, X. / Liu, X. / Wang, X. / Huang, S. / Cui, Q. / Feng, Y. / Liu, S.J. / Li, S.
History
DepositionJun 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2354
Polymers51,2141
Non-polymers1,0213
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.552, 86.552, 122.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cytochrome P450


Mass: 51214.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NSW2
#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-FW6 / (3-ethylphenyl) dihydrogen phosphate


Mass: 202.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2 M lithium chloride, 20% PEG3350, pH6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.796→50 Å / Num. obs: 12093 / % possible obs: 100 % / Redundancy: 24.6 % / Biso Wilson estimate: 42.44 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.02 / Rrim(I) all: 0.097 / Χ2: 1.002 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.9240.60611560.9730.1250.6190.983100
2.9-3.0226.20.47211770.980.0930.4811.002100
3.02-3.1526.10.3611920.9890.0710.3671.029100
3.15-3.3225.80.24811820.9940.0490.2531.068100
3.32-3.5325.40.18311890.9960.0370.1871.126100
3.53-3.824.50.12511980.9980.0260.1281.072100
3.8-4.1822.80.09111940.9980.0190.0931.044100
4.18-4.7924.70.06712270.9990.0140.0690.924100
4.79-6.0324.80.06212340.9990.0120.0630.829100
6.03-5021.70.06613440.9980.0140.0680.94799.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GWE

5gwe


Resolution: 2.8→43.281 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 1203 10 %
Rwork0.1974 10822 -
obs0.2027 12025 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.21 Å2 / Biso mean: 46.6991 Å2 / Biso min: 14.45 Å2
Refinement stepCycle: final / Resolution: 2.8→43.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 69 56 3341
Biso mean--38.83 33.05 -
Num. residues----405
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.90760.33491270.2602114899
2.9076-3.03980.33271310.25761170100
3.0398-3.20010.3171330.24381192100
3.2001-3.40050.2851320.22471190100
3.4005-3.66290.23221300.20171179100
3.6629-4.03130.27031320.17711197100
4.0313-4.61410.20871360.15831209100
4.6141-5.8110.21651360.17571231100
5.811-43.2810.21361460.1902130699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0221-0.20331.39252.41580.6193.5094-0.0686-0.19040.16540.0480.0046-0.2463-0.0024-0.15870.04660.17440.0524-0.02350.20290.06440.1861-37.1847-7.5828-14.6317
26.0621-1.1630.97874.6905-0.53119.4308-0.00161.07360.3246-1.3695-0.087-1.05230.6281.58860.09440.8586-0.20540.06230.66590.17220.6875-16.93533.3695-27.9975
31.35360.44360.56641.72781.15263.0933-0.1015-0.0169-0.0344-0.03860.2221-0.69950.01490.721-0.11610.25910.0865-0.00380.4580.01290.5578-14.6381-11.515-19.4718
42.22550.0398-0.27192.35270.14692.4505-0.19610.1691-0.3352-0.41090.1346-0.28420.25060.16930.02970.2713-0.00380.03410.2430.04580.2214-31.4871-15.5355-29.895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 114 )A24 - 114
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 135 )A115 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 282 )A136 - 282
4X-RAY DIFFRACTION4chain 'A' and (resid 283 through 428 )A283 - 428

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