[English] 日本語
Yorodumi
- PDB-5xjn: cytochrome P450 CREJ in complex with (4-ethylphenyl) dihydrogen p... -

+
Open data


ID or keywords:

Loading...

-
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


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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more