[English] 日本語
Yorodumi
- PDB-7pga: Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pga
TitleChimeric carminomycin-4-O-methyltransferase (DnrK) with regions from 10-hydroxylase RdmB and 10-decarboxylase TamK
ComponentsCarminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
KeywordsBIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / aclacinomycin 10-hydroxylase / tsukubarubicin 10-decarboxylase
Function / homology
Function and homology information


carminomycin 4-O-methyltransferase / daunorubicin biosynthetic process / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / O-methyltransferase activity / antibiotic biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Chem-VAK / Methyltransferase domain-containing protein / Carminomycin 4-O-methyltransferase DnrK / Aclacinomycin 10-hydroxylase RdmB
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
Streptomyces tsukubensis (bacteria)
Streptomyces purpurascens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsDinis, P. / MetsaKetela, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Pnas Nexus / Year: 2023
Title: Evolution-inspired engineering of anthracycline methyltransferases.
Authors: Dinis, P. / Tirkkonen, H. / Wandi, B.N. / Siitonen, V. / Niemi, J. / Grocholski, T. / Metsa-Ketela, M.
History
DepositionAug 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 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: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
B: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
C: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
D: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,18912
Polymers160,0024
Non-polymers3,1878
Water2,540141
1
A: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
B: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5946
Polymers80,0012
Non-polymers1,5944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-55 kcal/mol
Surface area25640 Å2
MethodPISA
2
C: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
D: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5946
Polymers80,0012
Non-polymers1,5944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-53 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.470, 102.640, 121.850
Angle α, β, γ (deg.)90.000, 98.230, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB / COMT / Anthracycline 4-O-methyltransferase / O-methyltransferase / 15-demethoxy-epsilon-rhodomycin ...COMT / Anthracycline 4-O-methyltransferase / O-methyltransferase / 15-demethoxy-epsilon-rhodomycin 10-hydroxylase / 15-demethoxyaclacinomycin T


Mass: 40000.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius (bacteria), (gene. exp.) Streptomyces tsukubensis (strain DSM 42081 / NBRC 108919 / NRRL 18488 / 9993) (bacteria), (gene. exp.) Streptomyces purpurascens (bacteria)
Gene: dnrK, STSU_011780, STSU_11775, rdmB / Strain: DSM 42081 / NBRC 108919 / NRRL 18488 / 9993 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q06528, UniProt: I2N5E8, UniProt: Q54527, carminomycin 4-O-methyltransferase, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-VAK / methyl (1R,2R,4S)-2-ethyl-2,4,5,7-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate / Aklavinone


Mass: 412.389 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C22H20O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.26 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M Sodium acetate, pH 4.6; 8% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryocooling / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9679 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9679 Å / Relative weight: 1
ReflectionResolution: 2.38→49.8 Å / Num. obs: 58153 / % possible obs: 98.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 30.89 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 7.4
Reflection shellResolution: 2.38→9.22 Å / Rmerge(I) obs: 0.963 / Num. unique obs: 5430

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TW2

1tw2


Resolution: 2.77→45.89 Å / SU ML: 0.3598 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.1002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2533 1998 5.41 %
Rwork0.2005 34929 -
obs0.2034 36927 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.06 Å2
Refinement stepCycle: LAST / Resolution: 2.77→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10173 0 224 141 10538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004710619
X-RAY DIFFRACTIONf_angle_d0.892514521
X-RAY DIFFRACTIONf_chiral_restr0.05521710
X-RAY DIFFRACTIONf_plane_restr0.00581862
X-RAY DIFFRACTIONf_dihedral_angle_d16.4153793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.840.34611440.27482527X-RAY DIFFRACTION99.85
2.84-2.920.34291430.24422499X-RAY DIFFRACTION99.89
2.92-30.27231440.23372515X-RAY DIFFRACTION99.11
3-3.10.31441420.23022482X-RAY DIFFRACTION98.61
3.1-3.210.3031450.22952522X-RAY DIFFRACTION98.41
3.21-3.340.30551410.22742466X-RAY DIFFRACTION98.64
3.34-3.490.28581410.23122494X-RAY DIFFRACTION98.69
3.49-3.670.30031430.20272506X-RAY DIFFRACTION98.44
3.67-3.90.23871420.18662467X-RAY DIFFRACTION97.94
3.9-4.210.23121360.18282376X-RAY DIFFRACTION93.49
4.21-4.630.18431390.15432441X-RAY DIFFRACTION95.2
4.63-5.30.2051450.16422530X-RAY DIFFRACTION99.33
5.3-6.670.21791460.20362546X-RAY DIFFRACTION99.67
6.67-45.890.19441470.17022558X-RAY DIFFRACTION98.01

+
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