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- PDB-9p2p: Streptomyces thermoviolaceus ClpC2 C-terminal domain dimer -

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Basic information

Entry
Database: PDB / ID: 9p2p
TitleStreptomyces thermoviolaceus ClpC2 C-terminal domain dimer
ComponentsATP-dependent Clp protease ATP-binding subunit ClpC2
KeywordsDNA BINDING PROTEIN / Dimer / Transcriptional repressor
Biological speciesStreptomyces thermoviolaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsAnderson, H.R. / 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.A. / Ogbonna, E.C. / Kandel, P. / Schmitz, K.R.
History
DepositionJun 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpC2


Theoretical massNumber of molelcules
Total (without water)19,0521
Polymers19,0521
Non-polymers00
Water2,522140
1
A: ATP-dependent Clp protease ATP-binding subunit ClpC2

A: ATP-dependent Clp protease ATP-binding subunit ClpC2


Theoretical massNumber of molelcules
Total (without water)38,1052
Polymers38,1052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2050 Å2
ΔGint-9 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.849, 46.065, 71.281
Angle α, β, γ (deg.)90.000, 105.526, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.75 / Details: 0.1 M Bis-tris, pH 5.75, 29% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 28906 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 13.15 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 63.78
Reflection shellResolution: 1.41→1.43 Å / Num. unique obs: 1415 / CC1/2: 0.734 / CC star: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→34.34 Å / SU ML: 0.1518 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.3126
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2141 1396 5.04 %
Rwork0.1893 26327 -
obs0.1905 27723 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.04 Å2
Refinement stepCycle: LAST / Resolution: 1.41→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 0 140 1250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211128
X-RAY DIFFRACTIONf_angle_d0.48721534
X-RAY DIFFRACTIONf_chiral_restr0.0467184
X-RAY DIFFRACTIONf_plane_restr0.0035200
X-RAY DIFFRACTIONf_dihedral_angle_d12.5889414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.460.2893970.29311718X-RAY DIFFRACTION63.04
1.46-1.520.30641400.25012608X-RAY DIFFRACTION95.35
1.52-1.590.25371360.22992756X-RAY DIFFRACTION99.97
1.59-1.670.2291540.21932695X-RAY DIFFRACTION100
1.67-1.780.22341380.21132745X-RAY DIFFRACTION100
1.78-1.910.23571450.20872740X-RAY DIFFRACTION100
1.91-2.110.22021390.1962741X-RAY DIFFRACTION100
2.11-2.410.18361510.17842761X-RAY DIFFRACTION100
2.41-3.040.22191400.17712772X-RAY DIFFRACTION99.69
3.04-34.340.19181560.16392791X-RAY DIFFRACTION99.66

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