[English] 日本語
Yorodumi
- PDB-5kyo: Crystal Structure of CYP101J2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kyo
TitleCrystal Structure of CYP101J2
ComponentsCYP101J2
KeywordsOXIDOREDUCTASE / cytochrome P450 monooxygenase / 1 / 8-cineole hydroxylation
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 monooxygenase
Similarity search - Component
Biological speciesSphingobium yanoikuyae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsUnterweger, B. / Drinkwater, N. / Dumsday, G.J. / McGowan, S.
CitationJournal: Proteins / Year: 2017
Title: X-ray crystal structure of cytochrome P450 monooxygenase CYP101J2 from Sphingobium yanoikuyae strain B2.
Authors: Unterweger, B. / Drinkwater, N. / Johanesen, P. / Lyras, D. / Dumsday, G.J. / McGowan, S.
History
DepositionJul 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYP101J2
B: CYP101J2
C: CYP101J2
D: CYP101J2
E: CYP101J2
F: CYP101J2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,24512
Polymers292,5466
Non-polymers3,6996
Water38,1922120
1
A: CYP101J2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3742
Polymers48,7581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYP101J2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3742
Polymers48,7581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CYP101J2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3742
Polymers48,7581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CYP101J2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3742
Polymers48,7581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: CYP101J2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3742
Polymers48,7581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: CYP101J2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3742
Polymers48,7581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.426, 100.031, 99.963
Angle α, β, γ (deg.)63.46, 63.66, 63.67
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
CYP101J2


Mass: 48757.691 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium yanoikuyae (bacteria) / Strain: B2 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A1C9CIU0*PLUS
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2120 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 19% PEG 6000, 0.1 M MES pH 6.0, 0.2 M LiCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→72.57 Å / Num. obs: 261465 / % possible obs: 95.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.3
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.838

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T85

1t85


Resolution: 1.8→42.601 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2763 11749 4.53 %
Rwork0.2234 --
obs0.2258 259482 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→42.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18232 0 258 2120 20610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819287
X-RAY DIFFRACTIONf_angle_d1.18226373
X-RAY DIFFRACTIONf_dihedral_angle_d13.2837126
X-RAY DIFFRACTIONf_chiral_restr0.0442880
X-RAY DIFFRACTIONf_plane_restr0.0063448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.36484250.34048109X-RAY DIFFRACTION93
1.8205-1.84190.37384490.32738105X-RAY DIFFRACTION93
1.8419-1.86430.36943650.32387988X-RAY DIFFRACTION93
1.8643-1.88790.42123520.32378255X-RAY DIFFRACTION94
1.8879-1.91280.35413430.30328211X-RAY DIFFRACTION94
1.9128-1.9390.34053670.27788132X-RAY DIFFRACTION94
1.939-1.96670.31423530.27478215X-RAY DIFFRACTION95
1.9667-1.9960.31313780.25948343X-RAY DIFFRACTION95
1.996-2.02720.28633560.24388289X-RAY DIFFRACTION95
2.0272-2.06050.29544060.24098261X-RAY DIFFRACTION95
2.0605-2.0960.29274080.23468250X-RAY DIFFRACTION95
2.096-2.13410.28744090.2418249X-RAY DIFFRACTION96
2.1341-2.17510.28953010.22568354X-RAY DIFFRACTION95
2.1751-2.21950.28733010.23868421X-RAY DIFFRACTION96
2.2195-2.26780.31754030.2388280X-RAY DIFFRACTION96
2.2678-2.32060.30383970.22718336X-RAY DIFFRACTION96
2.3206-2.37860.29643030.2338407X-RAY DIFFRACTION96
2.3786-2.44290.28654860.22328246X-RAY DIFFRACTION96
2.4429-2.51480.26995140.21568145X-RAY DIFFRACTION96
2.5148-2.59590.27884780.22038205X-RAY DIFFRACTION96
2.5959-2.68870.28454870.22548323X-RAY DIFFRACTION96
2.6887-2.79630.30393030.23638360X-RAY DIFFRACTION96
2.7963-2.92360.30094660.23148280X-RAY DIFFRACTION96
2.9236-3.07760.26164360.21478245X-RAY DIFFRACTION96
3.0776-3.27040.27583590.21058300X-RAY DIFFRACTION95
3.2704-3.52280.27224000.21048291X-RAY DIFFRACTION95
3.5228-3.87710.2623930.28179X-RAY DIFFRACTION95
3.8771-4.43760.22034980.18027873X-RAY DIFFRACTION93
4.4376-5.5890.22373280.18728440X-RAY DIFFRACTION96
5.589-42.6130.22862850.20878641X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -66.3091 Å / Origin y: -150.6374 Å / Origin z: 158.2347 Å
111213212223313233
T0.2031 Å20.0165 Å20.0107 Å2-0.1855 Å20.0047 Å2--0.1717 Å2
L0.0187 °2-0.0087 °2-0.0032 °2-0.0233 °2-0.0084 °2--0.0246 °2
S0.0122 Å °0.0252 Å °-0.0011 Å °0.0049 Å °-0.0042 Å °0.0257 Å °0.0251 Å °-0.0146 Å °-0.0078 Å °
Refinement TLS groupSelection details: all

+
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://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