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- PDB-9p39: Streptomyces thermoviolaceus ClpC2 C-terminal domain with bound p... -

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Basic information

Entry
Database: PDB / ID: 9p39
TitleStreptomyces thermoviolaceus ClpC2 C-terminal domain with bound phosphoarginine
ComponentsATP-dependent Clp protease ATP-binding subunit ClpC2
KeywordsDNA BINDING PROTEIN / Transcriptional regulator / phosphoarginine sensor
Function / homologyDI(HYDROXYETHYL)ETHER / phospho-arginine
Function and homology information
Biological speciesStreptomyces thermoviolaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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.R. / Ogbonna, E.C. / Kandel, P. / Schmitz, K.R.
History
DepositionJun 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5375
Polymers19,0521
Non-polymers4844
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.084, 74.084, 50.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-RPI / phospho-arginine


Type: L-peptide linking / Mass: 254.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris, pH 5.5, 1 mM pArg, and 2 M ammonium sulfate

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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 EIGER 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: 1.3→50 Å / Num. obs: 38875 / % possible obs: 99.8 % / Redundancy: 17.2 % / Biso Wilson estimate: 12.92 Å2 / CC1/2: 1 / Net I/σ(I): 69.38
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1911 / CC1/2: 0.741

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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: 1.3→39.77 Å / SU ML: 0.1217 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1897 3053 5.63 %
Rwork0.1676 51185 -
obs0.1689 35725 71.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.85 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 31 118 1318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861215
X-RAY DIFFRACTIONf_angle_d1.08741646
X-RAY DIFFRACTIONf_chiral_restr0.061195
X-RAY DIFFRACTIONf_plane_restr0.0083214
X-RAY DIFFRACTIONf_dihedral_angle_d13.5253446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.3455370.2952596X-RAY DIFFRACTION18.37
1.32-1.340.1935480.2483914X-RAY DIFFRACTION28.5
1.34-1.370.1923690.23261145X-RAY DIFFRACTION34.46
1.37-1.390.2476770.23661300X-RAY DIFFRACTION40.32
1.39-1.420.2451860.22971440X-RAY DIFFRACTION44.24
1.42-1.450.2986960.23121609X-RAY DIFFRACTION48.52
1.45-1.480.2468970.2221645X-RAY DIFFRACTION50.65
1.48-1.510.2128980.21871666X-RAY DIFFRACTION50.81
1.51-1.550.20031000.21441727X-RAY DIFFRACTION52.41
1.55-1.590.20871160.19021843X-RAY DIFFRACTION57
1.59-1.640.22111280.18342242X-RAY DIFFRACTION68.18
1.64-1.690.23251600.18512721X-RAY DIFFRACTION83.1
1.69-1.750.21171840.18163019X-RAY DIFFRACTION92.17
1.75-1.820.2221840.17433205X-RAY DIFFRACTION97.55
1.82-1.910.24011970.17553246X-RAY DIFFRACTION99.65
1.91-2.010.18421890.16013285X-RAY DIFFRACTION99.97
2.01-2.130.18841960.16213255X-RAY DIFFRACTION99.97
2.13-2.30.18231960.15483278X-RAY DIFFRACTION100
2.3-2.530.20111940.15463252X-RAY DIFFRACTION100
2.53-2.890.16611960.16023259X-RAY DIFFRACTION99.94
2.89-3.650.19362030.16593279X-RAY DIFFRACTION99.97
3.65-39.770.15342020.15363259X-RAY DIFFRACTION99.8

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