[English] 日本語
Yorodumi
- PDB-7oju: Chaetomium thermophilum Naa50 GNAT-domain in complex with bisubst... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oju
TitleChaetomium thermophilum Naa50 GNAT-domain in complex with bisubstrate analogue CoA-Ac-MVNAL
Components
  • MVNAL Peptide
  • N-acetyltransferase-like protein
KeywordsTRANSFERASE / N-alpha-acetyltransferase / GNAT-fold / Naa50 / Chaetomium thermophilum
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / cytoplasm
Similarity search - Function
: / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBOXYMETHYL COENZYME *A / N-acetyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsWeidenhausen, J. / Kopp, J. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586/6-1 Germany
German Research Foundation (DFG)201348542 - SFB 1036(TP22) Germany
CitationJournal: Int J Mol Sci / Year: 2022
Title: Extended N-Terminal Acetyltransferase Naa50 in Filamentous Fungi Adds to Naa50 Diversity.
Authors: Weidenhausen, J. / Kopp, J. / Ruger-Herreros, C. / Stein, F. / Haberkant, P. / Lapouge, K. / Sinning, I.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetyltransferase-like protein
H: MVNAL Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8479
Polymers24,2792
Non-polymers1,5687
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.936, 43.649, 140.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AH

#1: Protein N-acetyltransferase-like protein


Mass: 23732.049 Da / Num. of mol.: 1 / Mutation: N-terminal 81 aa & C-terminal 156 aa deletions
Source method: isolated from a genetically manipulated source
Details: Numbering is wrong: The protein was cloned with N- (81 aa) and C-terminal (156 aa) deletions. Therefore, the first leucine in the cloned sequence corresponds to residue number 82 (and not 3). ...Details: Numbering is wrong: The protein was cloned with N- (81 aa) and C-terminal (156 aa) deletions. Therefore, the first leucine in the cloned sequence corresponds to residue number 82 (and not 3). The N-terminal MG are due to cloning. Hexahistidine at the C-terminus is a His-tag.
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0014970 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0S1V5
#2: Protein/peptide MVNAL Peptide


Mass: 546.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 230 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 62 mg mL-1 protein mixed 1:2 with CoA-Ac-Lys; drops (600 nL): 1:1 mix of (20 mM HEPES pH 7.5, 500 mM NaCl) and (0.1 MES pH 6.0, 8 % (w/v) PEG3000, 37 % (v/v) PEG400). Crystals appeared after ...Details: 62 mg mL-1 protein mixed 1:2 with CoA-Ac-Lys; drops (600 nL): 1:1 mix of (20 mM HEPES pH 7.5, 500 mM NaCl) and (0.1 MES pH 6.0, 8 % (w/v) PEG3000, 37 % (v/v) PEG400). Crystals appeared after 1-2 days; 20 % (v/v) glycerol as cryo protectant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976246 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976246 Å / Relative weight: 1
ReflectionResolution: 1.1→41.67 Å / Num. obs: 92854 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 1 / Net I/σ(I): 18.01
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 9100 / CC1/2: 0.631 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSversion January 2019data reduction
Aimless7.0.072data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OB0

2ob0


Resolution: 1.1→41.67 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.165 4760 5.13 %
Rwork0.145 88086 -
obs0.146 92846 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.96 Å2 / Biso mean: 21.93 Å2 / Biso min: 7.94 Å2
Refinement stepCycle: final / Resolution: 1.1→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 160 223 2082
Biso mean--39.75 33.11 -
Num. residues----219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.110.28781530.267228883041100
1.11-1.130.23851570.23732873303099
1.13-1.140.24991620.218328673029100
1.14-1.150.21671530.20742904305799
1.15-1.170.23361650.198728733038100
1.17-1.180.2511570.195629173074100
1.18-1.20.20431600.182828743034100
1.2-1.220.21541450.176129293074100
1.22-1.240.19621530.172329183071100
1.24-1.260.17681460.172629013047100
1.26-1.280.20241730.169529253098100
1.28-1.30.19711650.164228873052100
1.3-1.330.16561600.163429153075100
1.33-1.360.18771490.152729223071100
1.36-1.390.16541610.138528953056100
1.39-1.420.15471530.132229453098100
1.42-1.450.16661640.11929123076100
1.45-1.490.16111660.121229133079100
1.49-1.540.14261600.123929343094100
1.54-1.590.13371600.121329343094100
1.59-1.640.16041650.120229183083100
1.64-1.710.13941790.115229183097100
1.71-1.790.14961520.119629903142100
1.79-1.880.14191300.117529533083100
1.88-20.14661730.118329613134100
2-2.150.11651280.119430053133100
2.15-2.370.13811680.12629663134100
2.37-2.710.15951520.139630343186100
2.71-3.420.16451800.145630263206100
3.42-41.670.18131710.172131893360100

+
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