[English] 日本語
Yorodumi
- PDB-8q6x: Crystal structure of Cytochrome P450 GymB5 from Streptomyces katrae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q6x
TitleCrystal structure of Cytochrome P450 GymB5 from Streptomyces katrae
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Nucleobase transferase / Cytochrome P450 / Mycocyclosin synthetase / prism-like fold
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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces katrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsFreytag, J. / Mueller, J.M. / Stehle, T. / Zocher, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)TRR261 Germany
CitationJournal: Chemcatchem / Year: 2024
Title: Intramolecular Coupling and Nucleobase Transfer - How Cytochrome P450 Enzymes GymBx Establish Their Chemoselectivity
Authors: Freytag, J. / Martin, A. / Muller, J.C. / Kelm, T. / Stehle, T. / Li, S.M. / Zocher, G.
History
DepositionAug 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3804
Polymers90,1472
Non-polymers1,2332
Water9,098505
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6902
Polymers45,0741
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6902
Polymers45,0741
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.166, 95.544, 81.459
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cytochrome P450


Mass: 45073.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces katrae (bacteria) / Gene: VR44_17910 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F4JF04
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate, 20 mM potassium sodium tartate, 20 mM sodium oxamate, 13% MPD, 13% PEG 1000, 13% PEG3350, 100 mM BIS-Tris pH 8.7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49.02 Å / Num. obs: 79072 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.99 / Rrim(I) all: 0.12 / Net I/σ(I): 10.9
Reflection shellResolution: 1.91→2.02 Å / Num. unique obs: 11329 / CC1/2: 0.57

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→49.02 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.227 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20818 2130 3 %RANDOM
Rwork0.16981 ---
obs0.17096 68841 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å2-1.03 Å2
2---1.57 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.91→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 86 505 6479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136146
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175718
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6638408
X-RAY DIFFRACTIONr_angle_other_deg1.421.57813206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0585777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.94521.678286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45215947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.521540
X-RAY DIFFRACTIONr_chiral_restr0.080.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026943
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021273
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_it2.553.2693111
X-RAY DIFFRACTIONr_mcbond_other2.5513.2673110
X-RAY DIFFRACTIONr_mcangle_it3.5124.893887
X-RAY DIFFRACTIONr_mcangle_other3.5124.8913888
X-RAY DIFFRACTIONr_scbond_it3.5793.6013035
X-RAY DIFFRACTIONr_scbond_other3.583.6013033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4525.2374521
X-RAY DIFFRACTIONr_long_range_B_refined6.42939.3416999
X-RAY DIFFRACTIONr_long_range_B_other6.40139.0616889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.957 Å
RfactorNum. reflection% reflection
Rfree0.356 154 -
Rwork0.358 4950 -
obs--98.82 %

+
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