[English] 日本語
Yorodumi
- PDB-9p4h: Streptomyces thermoviolaceus ClpC2 C-terminal domain with bound C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9p4h
TitleStreptomyces thermoviolaceus ClpC2 C-terminal domain with bound Cyclomarin A
Components
  • ATP-dependent Clp protease ATP-binding subunit ClpC2
  • LTU-WLU-ALA-WPA-VAL-MLE-WVL
KeywordsDNA BINDING PROTEIN / Transcriptional regulator / Antibiotic binder
Function / homology:
Function and homology information
Biological speciesStreptomyces thermoviolaceus (bacteria)
Streptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsAnderson, H.R. / Ogbonna, E.C. / Kandel, P. / Schmitz, K.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD26896 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM104316 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI171196 United States
CitationJournal: To Be Published
Title: Phosphoarginine modulates ClpC2 oligomerization and transcriptional regulation
Authors: Anderson, H.R. / Ogbonna, E.C. / Kandel, P. / Schmitz, K.R.
History
DepositionJun 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpC2
B: LTU-WLU-ALA-WPA-VAL-MLE-WVL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1763
Polymers20,1142
Non-polymers621
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.513, 44.061, 70.350
Angle α, β, γ (deg.)90.00, 109.36, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein ATP-dependent Clp protease ATP-binding subunit ClpC2


Mass: 19052.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces thermoviolaceus (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
#2: Protein/peptide LTU-WLU-ALA-WPA-VAL-MLE-WVL


Type: Peptide-like / Class: Antibiotic, Antimicrobial / Mass: 1061.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces sp. (bacteria) / References: BIRD: PRD_002419
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris, pH 5.75, 29% PEG3350, 1 mM Cyclomarin A

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 35083 / % possible obs: 98.8 % / Redundancy: 4.7 % / CC1/2: 0.998 / Net I/σ(I): 26.78
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 927 / CC1/2: 0.86

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→33.19 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 17.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1741 1605 5.03 %
Rwork0.148 --
obs0.1493 31894 76.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 4 169 1420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031293
X-RAY DIFFRACTIONf_angle_d0.6141764
X-RAY DIFFRACTIONf_dihedral_angle_d11.899488
X-RAY DIFFRACTIONf_chiral_restr0.036211
X-RAY DIFFRACTIONf_plane_restr0.004230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.3116650.22691264X-RAY DIFFRACTION34
1.6-1.650.23940.21521693X-RAY DIFFRACTION48
1.65-1.720.1791000.19921912X-RAY DIFFRACTION53
1.72-1.80.19941060.16792143X-RAY DIFFRACTION59
1.8-1.890.16561420.15422518X-RAY DIFFRACTION70
1.89-2.010.18051540.15093101X-RAY DIFFRACTION85
2.01-2.170.18021860.14913446X-RAY DIFFRACTION96
2.17-2.380.14941950.13473611X-RAY DIFFRACTION99
2.38-2.730.15291930.14653591X-RAY DIFFRACTION100
2.73-3.440.17631840.15023529X-RAY DIFFRACTION97
3.44-33.190.18061860.13263481X-RAY DIFFRACTION96

+
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