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- PDB-5xjn: cytochrome P450 CREJ in complex with (4-ethylphenyl) dihydrogen p... -

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Basic information

Entry
Database: PDB / ID: 5xjn
Titlecytochrome P450 CREJ in complex with (4-ethylphenyl) dihydrogen phosphate
ComponentsCytochrome P450
KeywordsELECTRON TRANSPORT / cytochrome P450 / Complex
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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(4-ethylphenyl) dihydrogen phosphate / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsDong, S. / Du, L. / Li, S. / Feng, Y.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31422002 China
Shandong Provincial Natural Science FoundationJQ201407 China
the 973 Project from Ministry of Science and Technology2012CB7211-04 China
National Natural Science Foundation of China31270784 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / 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
DepositionMay 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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)52,0333
Polymers51,2141
Non-polymers8192
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, it is monomer in liquid environment
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.070, 86.070, 125.040
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 / Fragment: UNP residues 25-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl0553 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NSW2
#2: Chemical ChemComp-88L / (4-ethylphenyl) dihydrogen phosphate


Mass: 202.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11O4P
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: PEG 3350, sodium iodide

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→41.68 Å / Num. obs: 52282 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 16.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.026 / Rrim(I) all: 0.094 / Net I/σ(I): 20.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.505 / Num. unique obs: 2731 / CC1/2: 0.958 / Rpim(I) all: 0.143 / Rrim(I) all: 0.525 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata collection
MOSFLMdata reduction
Aimless0.5.15data scaling
PHASERphasing
PHENIXmodel building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GWE

5gwe


Resolution: 1.7→35.449 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 1999 3.83 %
Rwork0.1815 50191 -
obs0.1825 52190 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.84 Å2 / Biso mean: 25.4763 Å2 / Biso min: 1.34 Å2
Refinement stepCycle: final / Resolution: 1.7→35.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 95 552 3854
Biso mean--13.14 35.85 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033398
X-RAY DIFFRACTIONf_angle_d0.7624634
X-RAY DIFFRACTIONf_chiral_restr0.042492
X-RAY DIFFRACTIONf_plane_restr0.004603
X-RAY DIFFRACTIONf_dihedral_angle_d10.2792027
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.26411410.209335433684100
1.7425-1.78960.22111410.204635473688100
1.7896-1.84230.24991390.204334893628100
1.8423-1.90170.26451420.223135703712100
1.9017-1.96970.24851410.212835383679100
1.9697-2.04860.21941420.184135703712100
2.0486-2.14180.21811400.1835393679100
2.1418-2.25470.19591430.181635573700100
2.2547-2.39590.21531420.17735773719100
2.3959-2.58090.22121440.178535833727100
2.5809-2.84050.21881430.175636113754100
2.8405-3.25130.19621440.179236223766100
3.2513-4.09530.18291480.155437003848100
4.0953-35.45640.1911490.18593745389497
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)
11.5596-0.1080.34751.86150.18491.7870.0038-0.0562-0.0472-0.00620.04710.26080.1186-0.2736-0.0430.1235-0.00630.0060.16680.04830.1447-42.6648-9.7104-19.1379
21.7256-0.18780.65011.6083-0.57441.7618-0.0695-0.03130.1152-0.00470.0397-0.0426-0.0880.02440.02040.12850.02430.01210.1029-0.00510.121-23.07940.2481-12.0727
33.06680.1569-0.22636.51611.25772.4477-0.07380.14450.0961-0.33560.2181-0.4697-0.27450.3138-0.04590.31760.03940.08320.3462-0.04760.3122-10.1228-15.5286-34.8657
41.05180.8282-0.0914.4430.24611.73240.1683-0.0682-0.55540.39540.0065-0.77910.30470.1877-0.16710.20220.0452-0.01450.15720.01430.2869-12.5133-20.5015-25.4941
50.73570.0780.19830.79040.07131.0047-0.0154-0.0256-0.0254-0.06460.0347-0.11460.01610.1335-0.01580.12740.01710.01680.12930.01650.1449-15.5365-6.5577-15.9923
61.3481-0.1335-0.42471.19230.3061.834-0.04460.0964-0.104-0.1660.02420.12330.1653-0.13260.02490.1746-0.0162-0.01660.11020.03650.1403-35.6777-10.9058-30.2248
71.0129-0.1509-0.40211.56460.6341.3832-0.03470.0765-0.2235-0.15210.0668-0.09890.28610.0623-0.0280.24680.02480.00720.1145-0.0080.1834-22.9671-23.2427-29.2379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 82 )A25 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 128 )A83 - 128
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 152 )A129 - 152
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 180 )A153 - 180
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 282 )A181 - 282
6X-RAY DIFFRACTION6chain 'A' and (resid 283 through 378 )A283 - 378
7X-RAY DIFFRACTION7chain 'A' and (resid 379 through 427 )A379 - 427

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