[English] 日本語
Yorodumi
- PDB-9ayn: Mycolicibacterium smegmatis ClpS with bound Ni2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ayn
TitleMycolicibacterium smegmatis ClpS with bound Ni2+
ComponentsATP-dependent Clp protease adapter protein ClpS
KeywordsPROTEIN BINDING / proteolysis / adaptor
Function / homologyATP-dependent Clp protease adaptor protein ClpS / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / protein catabolic process / peptidase activity / proteolysis / NICKEL (II) ION / ATP-dependent Clp protease adapter protein ClpS
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsPresloid, C.J. / Jiang, J. / Beardslee, P.C. / Anderson, H.R. / Swayne, T.M. / Schmitz, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM104316 United States
CitationJournal: Mol.Microbiol. / Year: 2025
Title: ClpS Directs Degradation of N-Degron Substrates With Primary Destabilizing Residues in Mycolicibacterium smegmatis.
Authors: Presloid, C.J. / Jiang, J. / Kandel, P. / Anderson, H.R. / Beardslee, P.C. / Swayne, T.M. / Schmitz, K.R.
History
DepositionMar 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease adapter protein ClpS
B: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3288
Polymers18,0442
Non-polymers2836
Water6,918384
1
A: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1644
Polymers9,0221
Non-polymers1423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1644
Polymers9,0221
Non-polymers1423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.493, 52.262, 54.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein ATP-dependent Clp protease adapter protein ClpS


Mass: 9022.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: clpS, MSMEG_4910 / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / References: UniProt: A0R1X7
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 12% PEG3350, 5 mM NiCl2 cryoprotected in 0.1 M HEPES pH 7.5, 40% PEG3350, 5 mM NiCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 0.97→27.32 Å / Num. obs: 87769 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 10.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 60.3
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 9.71 / Num. unique obs: 4327 / CC1/2: 0.8 / Rpim(I) all: 0.327 / Rrim(I) all: 0.76 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Coot0.9.8.92model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.97→27.32 Å / SU ML: 0.0951 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.8747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.139 4365 4.97 %
Rwork0.1185 83404 -
obs0.1195 87769 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.28 Å2
Refinement stepCycle: LAST / Resolution: 0.97→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 6 384 1628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081349
X-RAY DIFFRACTIONf_angle_d0.97641854
X-RAY DIFFRACTIONf_chiral_restr0.072206
X-RAY DIFFRACTIONf_plane_restr0.0088235
X-RAY DIFFRACTIONf_dihedral_angle_d14.4347504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.980.30891520.2852648X-RAY DIFFRACTION97.83
0.98-0.990.24221350.2472797X-RAY DIFFRACTION99.9
0.99-10.21961550.21872726X-RAY DIFFRACTION99.97
1-1.020.18511470.18862732X-RAY DIFFRACTION99.86
1.02-1.030.17951430.16762778X-RAY DIFFRACTION100
1.03-1.040.16411430.14872743X-RAY DIFFRACTION100
1.04-1.060.14621430.14022723X-RAY DIFFRACTION100
1.06-1.080.1411360.1282772X-RAY DIFFRACTION99.93
1.08-1.090.13181490.11752775X-RAY DIFFRACTION100
1.09-1.110.1431380.11492759X-RAY DIFFRACTION100
1.11-1.130.1331540.10812743X-RAY DIFFRACTION99.97
1.13-1.150.12831480.11152720X-RAY DIFFRACTION100
1.15-1.170.15381540.11852763X-RAY DIFFRACTION99.97
1.17-1.20.1391430.12162778X-RAY DIFFRACTION100
1.2-1.220.15051600.11752751X-RAY DIFFRACTION100
1.22-1.250.12981550.11392752X-RAY DIFFRACTION100
1.25-1.280.12991430.11272772X-RAY DIFFRACTION100
1.28-1.320.11811480.10812762X-RAY DIFFRACTION100
1.32-1.350.14531460.11142795X-RAY DIFFRACTION100
1.35-1.40.12281570.11272737X-RAY DIFFRACTION100
1.4-1.450.13241470.11942801X-RAY DIFFRACTION100
1.45-1.510.12921540.10972762X-RAY DIFFRACTION99.97
1.51-1.580.12151290.10792823X-RAY DIFFRACTION100
1.58-1.660.11531240.1112813X-RAY DIFFRACTION100
1.66-1.760.11361620.11382785X-RAY DIFFRACTION100
1.76-1.90.13221440.12562806X-RAY DIFFRACTION99.97
1.9-2.090.14151160.11692873X-RAY DIFFRACTION100
2.09-2.390.13131510.11462827X-RAY DIFFRACTION99.97
2.39-3.010.1691230.11582901X-RAY DIFFRACTION99.93
3.01-27.320.13471660.11072987X-RAY DIFFRACTION99.84

+
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