[English] 日本語
Yorodumi
- PDB-6f8a: Crystal structure of cytochrome P450 CYP260A1 (S276I) bound with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f8a
TitleCrystal structure of cytochrome P450 CYP260A1 (S276I) bound with histidine
ComponentsCytochrome P450 CYP260A1
KeywordsOXIDOREDUCTASE / Bacterial Proteins / Sorangium cellulosum / Cytochrome P-450 Enzyme System / Cytochrome P450 / Hydroxylation / Heme / Oxidation-Reduction / Progesterone / Histidine / Biocatalysis
Function / homology
Function and homology information


C-19 steroid 1alpha-hydroxylase / 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 / HISTIDINE / C-19 steroid 1alpha-hydroxylase
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsJozwik, I.K. / Thunnissen, A.M.W.H.
Funding support Germany, Netherlands, 2items
OrganizationGrant numberCountry
German Research FoundationBE 1343/23-1/23-2 Germany
European Commission289217 Netherlands
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Structure-Based Engineering of Steroidogenic CYP260A1 for Stereo- and Regioselective Hydroxylation of Progesterone.
Authors: Khatri, Y. / Jozwik, I.K. / Ringle, M. / Ionescu, I.A. / Litzenburger, M. / Hutter, M.C. / Thunnissen, A.W.H. / Bernhardt, R.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: Cytochrome P450 CYP260A1
B: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5936
Polymers89,0482
Non-polymers1,5454
Water13,745763
1
A: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2973
Polymers44,5241
Non-polymers7732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2973
Polymers44,5241
Non-polymers7732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.221, 65.151, 128.533
Angle α, β, γ (deg.)90.000, 112.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-115-

ARG

-
Components

#1: Protein Cytochrome P450 CYP260A1


Mass: 44523.977 Da / Num. of mol.: 2 / Mutation: S276I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (strain So ce56) (bacteria)
Strain: So ce56 / Gene: sce1588 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): C43
References: UniProt: A9FDB7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris propane pH 6.5, 16% (w/v) PEG 3350, 0.2 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91165 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 1.35→46.65 Å / Num. obs: 167978 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.029 / Rrim(I) all: 0.058 / Net I/σ(I): 14.7 / Num. measured all: 632864
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.35-1.373.60.3132995982960.9080.1920.3693.899.7
7.39-46.653.90.044430110900.9950.0260.05133.699.4

-
Processing

Software
NameVersionClassification
PHENIXrefinement
EDNAdata collection
XDSdata reduction
Aimless0.5.1data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5liv

5liv


Resolution: 1.35→46.65 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 16858 5.1 %
Rwork0.1782 313589 -
obs0.179 167978 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.31 Å2 / Biso mean: 18.9349 Å2 / Biso min: 4.98 Å2
Refinement stepCycle: final / Resolution: 1.35→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 0 194 768 7100
Biso mean--12.35 26.61 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116610
X-RAY DIFFRACTIONf_angle_d1.1859040
X-RAY DIFFRACTIONf_chiral_restr0.076974
X-RAY DIFFRACTIONf_plane_restr0.0071181
X-RAY DIFFRACTIONf_dihedral_angle_d14.632460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.36530.24875830.24741049311076100
1.3653-1.38140.26516300.24331028210912100
1.3814-1.39830.27665920.24411068411276100
1.3983-1.4160.285350.2351030810843100
1.416-1.43460.24945010.2266105851108699
1.4346-1.45420.24445720.22521037410946100
1.4542-1.4750.24426220.2177104871110999
1.475-1.4970.23175560.2131043010986100
1.497-1.52040.22936200.2056103811100199
1.5204-1.54540.22135630.2017104551101899
1.5454-1.5720.21115610.2059103501091198
1.572-1.60060.21055300.1971102451077598
1.6006-1.63140.22335900.18791049411084100
1.6314-1.66470.20255630.19071050611069100
1.6647-1.70090.225920.18851037610968100
1.7009-1.74050.22834990.18631050511004100
1.7405-1.7840.19895860.18031054111127100
1.784-1.83220.18915470.18071055311100100
1.8322-1.88610.2026000.17781037510975100
1.8861-1.9470.20945630.1809105141107799
1.947-2.01660.19685150.1809102791079498
2.0166-2.09730.20245420.17141047311015100
2.0973-2.19280.18575720.16851047911051100
2.1928-2.30840.18555430.16371054111084100
2.3084-2.4530.17485490.16491048511034100
2.453-2.64240.19715260.1687104901101699
2.6424-2.90830.18684690.1783104691093899
2.9083-3.3290.18176360.17091049311129100
3.329-4.19380.16755720.15721044511017100
4.1938-46.67870.16245290.1659104971102699

+
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