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- PDB-9q5p: Structure of the ClpC1-N-terminal domain of M. tuberculosis compl... -

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Basic information

Entry
Database: PDB / ID: 9q5p
TitleStructure of the ClpC1-N-terminal domain of M. tuberculosis complexed with P-Arginine bound to site no.2
ComponentsATP-dependent Clp protease ATP-binding subunit ClpC1
KeywordsCHAPERONE / ClpC1 ATPase / Rufomycin / Antibiotic / ClpC1-NTD-complex / CHAPERONE-ANTIBIOTIC complex
Function / homology
Function and homology information


protein folding chaperone / peptidoglycan-based cell wall / protein homodimerization activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / Clp repeat (R) N-terminal domain / Clp repeat (R) domain profile. / Clp, repeat (R) domain ...UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / Clp repeat (R) N-terminal domain / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
phospho-arginine / ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsAbad-Zapatero, C. / Wolf, N.M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Other governmentS2014-202 Japan
Other governmentH2018-202 Japan
Citation
Journal: To Be Published
Title: Isolation, Structural Characterization, and Biological Activity of Novel Terpenoid Natural Products Active Against Mycobacterium tuberculosis.
Authors: Abad-Zapatero, C. / Ratia, K.M. / Lee, H. / Franzblau, S.G. / Shetye, G. / Kaneko, T.
#1: Journal: Acs Infect Dis. / Year: 2019
Title: High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads.
Authors: Wolf, N.M. / Lee, H. / Choules, M.P. / Pauli, G.F. / Phansalkar, R. / Anderson, J.R. / Gao, W. / Ren, J. / Santarsiero, B.D. / Lee, H. / Cheng, J. / Jin, Y.Y. / Ho, N.A. / Duc, N.M. / Suh, J. ...Authors: Wolf, N.M. / Lee, H. / Choules, M.P. / Pauli, G.F. / Phansalkar, R. / Anderson, J.R. / Gao, W. / Ren, J. / Santarsiero, B.D. / Lee, H. / Cheng, J. / Jin, Y.Y. / Ho, N.A. / Duc, N.M. / Suh, J.W. / Abad-Zapatero, C. / Cho, S.
#2: Journal: J.Nat.Prod. / Year: 2025
Title: Structure-Based Analysis of Semisynthetic Anti-TB Rufomycin Analogues.
Authors: Zhou, B. / Shetye, G. / Klein, L.L. / Wolf, N.M. / Lee, H. / McAlpine, J.B. / Harris, G. / Chen, S.N. / Suh, J.W. / Cho, S.H. / Franzblau, S.G. / Abad-Zapatero, C. / Pauli, G.F.
History
DepositionAug 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 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 ClpC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2452
Polymers15,9901
Non-polymers2541
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, The ligand, Phosphorylated Arginine was bound at site2, using protein construct without His-tag. Related entry9Q3Z, is a complex with the same Protein ClpC1-NTD ...Evidence: surface plasmon resonance, The ligand, Phosphorylated Arginine was bound at site2, using protein construct without His-tag. Related entry9Q3Z, is a complex with the same Protein ClpC1-NTD but with a construct that contains a His tag at the C-terminus.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.470, 54.520, 71.430
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

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Components

#1: Protein ATP-dependent Clp protease ATP-binding subunit ClpC1


Mass: 15990.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpC1, Rv3596c, MTCY07H7B.26 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPC9
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: MCSG-1 E12, 2.5 M sodium Malonate pH 7, 1:1 ration of reservoir ClpC1-NTD-P-Arg sample
PH range: 7.0-7.4 / Temp details: 16 C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 22, 2022
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 1.33→43.34 Å / Num. obs: 38048 / % possible obs: 98.68 % / Redundancy: 3.4 % / Biso Wilson estimate: 8.13 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.092 / Rrim(I) all: 0.184 / Rsym value: 0.15 / Net I/σ(I): 5.8
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3786 / CC1/2: 0.974 / Rpim(I) all: 0.774 / Rrim(I) all: 1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→43.34 Å / SU ML: 0.1255 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1837 1919 5.05 %
Rwork0.1688 36069 -
obs0.1696 37988 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.67 Å2
Refinement stepCycle: LAST / Resolution: 1.33→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 16 158 1299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091176
X-RAY DIFFRACTIONf_angle_d1.181593
X-RAY DIFFRACTIONf_chiral_restr0.0663185
X-RAY DIFFRACTIONf_plane_restr0.009207
X-RAY DIFFRACTIONf_dihedral_angle_d6.7631174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.370.29931240.27332577X-RAY DIFFRACTION99.45
1.37-1.40.26511280.26612562X-RAY DIFFRACTION99.41
1.4-1.450.24661360.24212559X-RAY DIFFRACTION99.63
1.45-1.490.2311470.23442521X-RAY DIFFRACTION99.26
1.49-1.550.18811450.20432538X-RAY DIFFRACTION98.53
1.55-1.610.20841260.18332557X-RAY DIFFRACTION97.6
1.61-1.680.22291440.18272495X-RAY DIFFRACTION97.74
1.68-1.770.18981280.16782607X-RAY DIFFRACTION99.42
1.77-1.880.19161410.15422573X-RAY DIFFRACTION99.3
1.88-2.030.14961380.14282587X-RAY DIFFRACTION99.16
2.03-2.230.15141380.12712578X-RAY DIFFRACTION98.94
2.23-2.550.14081340.1322602X-RAY DIFFRACTION98.31
2.55-3.210.16941400.15362522X-RAY DIFFRACTION95.14
3.21-43.340.17691500.16472791X-RAY DIFFRACTION99.73

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