[English] 日本語
Yorodumi
- PDB-6r00: OphA DeltaC6 V404F complex with SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r00
TitleOphA DeltaC6 V404F complex with SAH
Components
  • PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY
  • Peptide N-methyltransferase
KeywordsTRANSFERASE / Peptide bond N-methyltransferase
Function / homologyTetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase/ribosomally synthesized cyclic peptide omphalotin A precursor ophMA
Function and homology information
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsSong, H. / Naismith, J.H.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Substrate Plasticity of a Fungal Peptide alpha-N-Methyltransferase.
Authors: Song, H. / Fahrig-Kamarauskaite, J.R. / Matabaro, E. / Kaspar, H. / Shirran, S.L. / Zach, C. / Pace, A. / Stefanov, B.A. / Naismith, J.H. / Kunzler, M.
History
DepositionMar 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _software.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptide N-methyltransferase
B: PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9633
Polymers46,5792
Non-polymers3841
Water4,107228
1
A: Peptide N-methyltransferase
B: PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY
hetero molecules

A: Peptide N-methyltransferase
B: PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9276
Polymers93,1584
Non-polymers7692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17810 Å2
ΔGint-114 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.772, 91.828, 162.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

21A-726-

HOH

31A-824-

HOH

-
Components

#1: Protein Peptide N-methyltransferase


Mass: 45048.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia (bacteria) / References: UniProt: A0A2R2JFI5
#2: Protein/peptide PHE-PRO-TRP-MVA-ILE-MVA-PHE-GLY-VAL-ILE-GLY-VAL-ILE-GLY


Mass: 1530.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2R2JFI5*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 0.1 M Bicine pH 9, 1.8-2.2 M Sodium malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.74→81.5 Å / Num. all: 733818 / Num. obs: 65997 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Net I/σ(I): 32.8
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3262 / CC1/2: 0.799 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0O

5n0o


Resolution: 1.74→81.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.691 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19206 3262 4.9 %RANDOM
Rwork0.17434 ---
obs0.17523 62734 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 42.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.74→81.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3085 0 26 229 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133215
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172972
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6484382
X-RAY DIFFRACTIONr_angle_other_deg1.3931.5736902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9015400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47222.236161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18115511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.221520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023634
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02657
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_it2.8392.8181608
X-RAY DIFFRACTIONr_mcbond_other2.7912.8131606
X-RAY DIFFRACTIONr_mcangle_it3.9144.2082010
X-RAY DIFFRACTIONr_mcangle_other3.9144.2082010
X-RAY DIFFRACTIONr_scbond_it3.8423.2061606
X-RAY DIFFRACTIONr_scbond_other3.8273.2051606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6624.6452372
X-RAY DIFFRACTIONr_long_range_B_refined7.60234.3613560
X-RAY DIFFRACTIONr_long_range_B_other7.56333.9133516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.742→1.787 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 218 -
Rwork0.257 4594 -
obs--100 %
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)
10.4329-0.1433-0.0041.3834-0.07480.4966-0.056-0.01630.0277-0.12880.0986-0.0717-0.0245-0.013-0.04260.0890.02730.00170.0290.00110.03730.33551.020827.6863
23.25610.4153-2.57854.313-0.81744.3496-0.20430.2305-0.0862-0.3546-0.11180.1203-0.1701-0.31050.31610.20960.0155-0.09820.1418-0.01610.1682-4.253318.48721.8815
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 501
2X-RAY DIFFRACTION2B398 - 411

+
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