[English] 日本語
Yorodumi
- PDB-7q6x: OleP mutant S240Y in complex with 6DEB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q6x
TitleOleP mutant S240Y in complex with 6DEB
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Oleandomicine / OleP / mutant / 6DEB
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
6-DEOXYERYTHRONOLIDE B / FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSavino, C. / Montemiglio, L.C. / Vallone, B. / Exertier, C. / Freda, I. / Gugole, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomolecules / Year: 2021
Title: Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics.
Authors: Montemiglio, L.C. / Gugole, E. / Freda, I. / Exertier, C. / D'Auria, L. / Chen, C.G. / Nardi, A.N. / Cerutti, G. / Parisi, G. / D'Abramo, M. / Savino, C. / Vallone, B.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 6, 2022Group: Advisory / Derived calculations / Structure summary
Category: entity_name_com / pdbx_validate_close_contact ...entity_name_com / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P-450
B: Cytochrome P-450
C: Cytochrome P-450
D: Cytochrome P-450
E: Cytochrome P-450
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,59224
Polymers269,2986
Non-polymers6,29418
Water4,035224
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0246
Polymers44,8831
Non-polymers1,1415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8863
Polymers44,8831
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9324
Polymers44,8831
Non-polymers1,0493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9324
Polymers44,8831
Non-polymers1,0493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9324
Polymers44,8831
Non-polymers1,0493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8863
Polymers44,8831
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)248.624, 110.355, 160.046
Angle α, β, γ (deg.)90.00, 129.63, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Cytochrome P-450


Mass: 44882.938 Da / Num. of mol.: 6 / Mutation: S240Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59819
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-DEB / 6-DEOXYERYTHRONOLIDE B


Mass: 386.523 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H38O6
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: Sodium Formate, 4.4 M

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2020
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→51.34 Å / Num. obs: 225386 / % possible obs: 99.2 % / Redundancy: 4 % / CC1/2: 0.992 / Net I/σ(I): 5.59
Reflection shellResolution: 2.5→2.65 Å / Num. unique obs: 36239 / CC1/2: 0.1 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mns

5mns


Resolution: 2.7→51.34 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 19.676 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 1.233 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26804 4388 4.8 %RANDOM
Rwork0.20414 ---
obs0.20721 87164 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.582 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å2-0.23 Å2
2--1.84 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.7→51.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18627 0 438 224 19289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01321198
X-RAY DIFFRACTIONr_bond_other_d0.0020.01720225
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.67629269
X-RAY DIFFRACTIONr_angle_other_deg1.2351.58846696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80752793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31720.1661325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.137153526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.38815261
X-RAY DIFFRACTIONr_chiral_restr0.0680.22750
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224475
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025047
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3486.86810030
X-RAY DIFFRACTIONr_mcbond_other3.3486.86810031
X-RAY DIFFRACTIONr_mcangle_it5.42510.31512643
X-RAY DIFFRACTIONr_mcangle_other5.42410.31612644
X-RAY DIFFRACTIONr_scbond_it3.0287.1311168
X-RAY DIFFRACTIONr_scbond_other3.0267.12811163
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.03610.59116407
X-RAY DIFFRACTIONr_long_range_B_refined7.74177.08322516
X-RAY DIFFRACTIONr_long_range_B_other7.7477.08222513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.518 386 -
Rwork0.489 6347 -
obs--99.97 %

+
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://pdbjlc1.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