[English] 日本語
Yorodumi
- PDB-8bii: O-Methyltransferase Plu4895 (mutant H229N) in complex with SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bii
TitleO-Methyltransferase Plu4895 (mutant H229N) in complex with SAH
Componentsmethyltransferase Plu4895 H229N mutant
KeywordsTRANSFERASE / methyltransferase / polyketide / anthraquinone
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
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 / Methyltransferase
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 Plu4895 H229N mutant
B: methyltransferase Plu4895 H229N mutant
C: methyltransferase Plu4895 H229N mutant
D: methyltransferase Plu4895 H229N mutant
E: methyltransferase Plu4895 H229N mutant
F: methyltransferase Plu4895 H229N mutant
G: methyltransferase Plu4895 H229N mutant
H: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,40517
Polymers307,2948
Non-polymers3,1119
Water93752
1
A: methyltransferase Plu4895 H229N mutant
B: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5924
Polymers76,8242
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-42 kcal/mol
Surface area25870 Å2
MethodPISA
2
C: methyltransferase Plu4895 H229N mutant
H: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5924
Polymers76,8242
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-42 kcal/mol
Surface area25180 Å2
MethodPISA
3
D: methyltransferase Plu4895 H229N mutant
hetero molecules

G: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5924
Polymers76,8242
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6640 Å2
ΔGint-39 kcal/mol
Surface area25570 Å2
MethodPISA
4
E: methyltransferase Plu4895 H229N mutant
F: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6285
Polymers76,8242
Non-polymers8043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-47 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.920, 98.300, 531.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
methyltransferase Plu4895 H229N mutant


Mass: 38411.805 Da / Num. of mol.: 8 / Mutation: H229N
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: A0A6L9JQS9
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium citrate, 0.1 M bis-tris propane pH 7.5, 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: Oct 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49 Å / Num. obs: 76974 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7541

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BIG

8big


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / SU B: 46.471 / SU ML: 0.394 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28129 3845 5 %RANDOM
Rwork0.23505 ---
obs0.23734 73065 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.643 Å2
Baniso -1Baniso -2Baniso -3
1--3.56 Å2-0 Å20 Å2
2--2.37 Å2-0 Å2
3---1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20366 0 209 52 20627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01320998
X-RAY DIFFRACTIONr_bond_other_d0.0010.01620079
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.62828369
X-RAY DIFFRACTIONr_angle_other_deg1.0311.58646367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68352529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5724.1371037
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.189153856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8131572
X-RAY DIFFRACTIONr_chiral_restr0.0340.22745
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0223464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024600
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_it0.7175.14610167
X-RAY DIFFRACTIONr_mcbond_other0.7175.14610167
X-RAY DIFFRACTIONr_mcangle_it1.347.71812679
X-RAY DIFFRACTIONr_mcangle_other1.347.71812680
X-RAY DIFFRACTIONr_scbond_it0.3575.12810831
X-RAY DIFFRACTIONr_scbond_other0.3575.12810831
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7377.67315691
X-RAY DIFFRACTIONr_long_range_B_refined2.49558.07322760
X-RAY DIFFRACTIONr_long_range_B_other2.49458.07322760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 274 -
Rwork0.336 5204 -
obs--99.42 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4505-0.099-0.35570.30170.30541.60350.0149-0.16930.1141-0.037-0.0858-0.0114-0.02170.05840.0710.2337-0.0554-0.03110.4183-0.0520.1825-9.1893-26.6316121.6029
20.62580.0073-0.61210.25830.39271.9453-0.1701-0.0173-0.30590.0234-0.0022-0.0431-0.02870.08560.17230.1761-0.01190.02760.33680.01690.31572.94-46.308891.7776
30.6432-0.2511-0.53980.20120.12462.59550.0585-0.15790.0788-0.1505-0.01690.00050.1096-0.1021-0.04170.3122-0.06210.02440.2719-0.0520.2185-22.8641-52.736953.7009
40.42620.0038-0.55730.2090.21981.81510.0395-0.01030.01020.0072-0.05350.13140.0011-0.05090.0140.4682-0.05420.00850.0543-0.03240.317712.808-78.222138.2569
50.23260.07110.57520.80170.10851.6994-0.08560.01570.0148-0.0650.0861-0.0064-0.02280.2193-0.00040.2209-0.04010.05350.4934-0.0730.140123.5583-99.4638106.7637
60.16820.12940.27220.5288-0.09862.1053-0.0377-0.09930.0853-0.3390.10610.20370.00760.0924-0.06840.4814-0.1172-0.03330.24450.00960.19922.5007-103.296775.2983
70.2347-0.1846-0.58210.77160.48741.5732-0.0512-0.0745-0.0294-0.12630.0013-0.06520.14260.11580.04990.5120.0091-0.03840.06510.05060.2887-22.7494-92.663712.5617
80.45190.1814-0.1780.2275-0.6352.36210.0255-0.03030.0974-0.0449-0.00630.0065-0.1694-0.0084-0.01910.60030.00070.08970.0024-0.01240.2276-15.9123-35.438721.0372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 900
2X-RAY DIFFRACTION2B0 - 900
3X-RAY DIFFRACTION3C0 - 900
4X-RAY DIFFRACTION4D0 - 900
5X-RAY DIFFRACTION5E0 - 401
6X-RAY DIFFRACTION6F0 - 900
7X-RAY DIFFRACTION7G0 - 900
8X-RAY DIFFRACTION8H0 - 900

+
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