[English] 日本語
Yorodumi
- PDB-8bib: O-Methyltransferase Plu4890 in complex with SAH and AQ-256 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bib
TitleO-Methyltransferase Plu4890 in complex with SAH and AQ-256
ComponentsMethyltransferase Plu4890
KeywordsTRANSFERASE / methyltransferase / polyketide / anthraquinone
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
CARBONATE ION / 1,3,8-tris(oxidanyl)anthracene-9,10-dione / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuber, E.M. / Groll, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments.
Authors: Huber, E.M. / Kreling, L. / Heinrich, A.K. / Dunnebacke, M. / Pothig, A. / Bode, H.B. / Groll, M.
History
DepositionNov 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 17, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyltransferase Plu4890
B: Methyltransferase Plu4890
C: Methyltransferase Plu4890
D: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,22621
Polymers146,2024
Non-polymers3,02417
Water8,827490
1
A: Methyltransferase Plu4890
B: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,61710
Polymers73,1012
Non-polymers1,5168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-41 kcal/mol
Surface area25620 Å2
MethodPISA
2
D: Methyltransferase Plu4890
hetero molecules

C: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,60911
Polymers73,1012
Non-polymers1,5089
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_344-x-2,y-1/2,-z-11
Buried area6920 Å2
ΔGint-59 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.060, 77.050, 167.220
Angle α, β, γ (deg.)90.000, 95.500, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Methyltransferase Plu4890


Mass: 36550.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6L9JR93

-
Non-polymers , 7 types, 507 molecules

#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
#3: Chemical
ChemComp-QOI / 1,3,8-tris(oxidanyl)anthracene-9,10-dione


Mass: 256.210 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M NaI, 0.1 M bis-tris propane pH 6.5, 20% PEG3350

-
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: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48 Å / Num. obs: 68830 / % possible obs: 96.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.1
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2 / Num. unique obs: 8321

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BGT
Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.196 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 3440 5 %RANDOM
Rwork0.2136 ---
obs0.2155 65359 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 276 Å2 / Biso mean: 45.363 Å2 / Biso min: 26.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å21.08 Å2
2--1 Å2-0 Å2
3----3.32 Å2
Refinement stepCycle: final / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10296 0 206 492 10994
Biso mean--42.31 51.3 -
Num. residues----1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310725
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179750
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.63914465
X-RAY DIFFRACTIONr_angle_other_deg1.0841.58122622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77851272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62522.897580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.831151888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6711556
X-RAY DIFFRACTIONr_chiral_restr0.0380.21332
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022356
X-RAY DIFFRACTIONr_rigid_bond_restr0.233320475
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 255 -
Rwork0.277 4849 -
all-5104 -
obs--98.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0975-0.0195-0.07080.0369-0.06620.2775-0.0099-0.01820.00610.00440.00850.0037-0.01060.0160.00140.01350.0015-0.02690.0154-0.00430.0612-40.0295-11.045317.222
20.0832-0.0287-0.04320.03310.04540.2581-0.01330.00720.0001-0.00410.01070.0041-0.0083-0.01110.00260.0147-0.0057-0.02570.01180.00280.0627-52.7484-11.889-18.2531
30.12770.04960.0650.02120.02940.12440.0133-0.0157-0.00830.0045-0.0113-0.0023-0.0022-0.007-0.0020.0105-0.0027-0.02420.01790.00340.0648-35.98026.4299-64.34
40.0985-0.01920.08260.0150.0090.1330.0076-0.0032-0.0084-0.0001-0.0023-0.00050.00620.0031-0.00540.0087-0.0029-0.02260.02110.00320.0616-66.088-32.912-65.2119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 402
2X-RAY DIFFRACTION2B0 - 402
3X-RAY DIFFRACTION3C0 - 402
4X-RAY DIFFRACTION4D0 - 402

+
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://pdbjlvh1.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