[English] 日本語
Yorodumi
- PDB-6qzz: full length OphA V404E in complex with SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qzz
Titlefull length OphA V404E in complex with SAH
Components(Peptide N-methyltransferase) x 2
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: 1.85 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 / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptide N-methyltransferase
B: Peptide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1554
Polymers91,3862
Non-polymers7692
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15370 Å2
ΔGint-90 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.002, 91.723, 85.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SAHSAHAA - C7 - 5016
2SERSERBB7 - 4126 - 411

-
Components

#1: Protein Peptide N-methyltransferase


Mass: 45678.844 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
#2: Protein Peptide N-methyltransferase


Mass: 45706.898 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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.7 Å3/Da / Density % sol: 66.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3-0.4 M KSCN, 0.1 M Bicine pH 9, 1.8-2.3 M Sodium malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.85→80.1 Å / Num. all: 798741 / Num. obs: 110277 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Net I/σ(I): 16.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2 / Num. unique obs: 5363 / CC1/2: 0.621 / % possible all: 98.4

-
Processing

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

5n0o


Resolution: 1.85→80.05 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.964 / SU B: 6.39 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22462 5568 5.1 %RANDOM
Rwork0.20638 ---
obs0.20731 104622 99.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 50.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.91 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→80.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 52 326 6461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136353
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175872
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.6488660
X-RAY DIFFRACTIONr_angle_other_deg1.271.57413646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0622.31316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.355151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2211539
X-RAY DIFFRACTIONr_chiral_restr0.0630.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021284
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_it4.413.0553177
X-RAY DIFFRACTIONr_mcbond_other4.413.0553177
X-RAY DIFFRACTIONr_mcangle_it5.3824.5493973
X-RAY DIFFRACTIONr_mcangle_other5.3824.5493974
X-RAY DIFFRACTIONr_scbond_it5.8673.5343176
X-RAY DIFFRACTIONr_scbond_other5.8673.5353176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9295.114688
X-RAY DIFFRACTIONr_long_range_B_refined9.72337.7787060
X-RAY DIFFRACTIONr_long_range_B_other9.72337.416986
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12030 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 449 -
Rwork0.349 7547 -
obs--98.9 %
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)
10.44810.06010.05962.4121-0.20780.7729-0.0449-0.00970.00170.08520.1168-0.4032-0.0151-0.0422-0.0720.0277-0.0099-0.01630.09330.00410.0883-27.51130.3144-21.3551
20.4165-0.10470.08222.3486-0.19380.6828-0.05860.01850.0185-0.08620.1297-0.38070.0393-0.0474-0.07110.0279-0.01080.00210.08750.00060.0828-27.5998-0.8479-21.6563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 501
2X-RAY DIFFRACTION2B7 - 501

+
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