[English] 日本語
Yorodumi
- PDB-8r2e: X-ray crystallographic structure of SnoaL2 in complex with the po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r2e
TitleX-ray crystallographic structure of SnoaL2 in complex with the polyketide reaction product
ComponentsSnoL
KeywordsBIOSYNTHETIC PROTEIN / Polyketide / antibiotic / biosynthesis
Function / homologypolyketide metabolic process / SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / NTF2-like domain superfamily / : / SnoL
Function and homology information
Biological speciesStreptomyces nogalater (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchnell, R. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03999 Sweden
CitationJournal: Acs Catalysis / Year: 2024
Title: Mechanism of Two-Component Mono-Oxygenases Involved in Anthracycline 1-Hydroxylation
Authors: Wandi, B.N. / Dinis, P. / Siitonen, V. / Schneider, G. / Schnell, R. / Metsa-Ketele, M.
History
DepositionNov 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SnoL
B: SnoL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4153
Polymers33,8262
Non-polymers5891
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The same type of homodimers are commonin the protein family
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-6 kcal/mol
Surface area12120 Å2
Unit cell
Length a, b, c (Å)52.960, 62.195, 89.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SnoL


Mass: 16913.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His6-tag used in affinity purification / Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: snoL / Plasmid: pBAD
Details (production host): N-terminal His6-tag, not removable
Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9RN64
#2: Chemical ChemComp-XN8 / 3',4'-demethoxy-nogalose-1-hydroxy-nogalamycinone / methyl (1R,2S,4S)-4-[(2R,3R,4R,5S,6S)-3-methoxy-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-methyl-2,5,7,10-tetrakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1H-tetracene-1-carboxylate


Mass: 588.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32O13 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 39 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.2 M MgCl2, 25% PEG3350, ligand at 2 mM

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2018 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2→36.77 Å / Num. obs: 19854 / % possible obs: 96.7 % / Observed criterion σ(I): 1.5 / Redundancy: 2.1 % / Biso Wilson estimate: 52.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.07 / Net I/σ(I): 9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1348 / CC1/2: 0.529 / Rpim(I) all: 0.583 / % possible all: 89.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.44 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23821 947 4.8 %RANDOM
Rwork0.1946 ---
obs0.19673 18877 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.125 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å2-0 Å20 Å2
2---2.11 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 42 203 2310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192163
X-RAY DIFFRACTIONr_bond_other_d0.0030.021993
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9412950
X-RAY DIFFRACTIONr_angle_other_deg1.0243.0054555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8595255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69922.523107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23915341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8821523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.0212425
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02528
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_it2.5473.0171026
X-RAY DIFFRACTIONr_mcbond_other2.5413.0131025
X-RAY DIFFRACTIONr_mcangle_it3.5854.5031279
X-RAY DIFFRACTIONr_mcangle_other3.5894.5071280
X-RAY DIFFRACTIONr_scbond_it3.5293.4371137
X-RAY DIFFRACTIONr_scbond_other3.5283.4381138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3374.9971672
X-RAY DIFFRACTIONr_long_range_B_refined7.51729.5169343
X-RAY DIFFRACTIONr_long_range_B_other7.43829.3449197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 61 -
Rwork0.278 1279 -
obs--89.16 %

+
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