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- PDB-3wdc: N-terminal domain of Mycobacterium tuberculosis ClpC1 bound to Cy... -

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Basic information

Entry
Database: PDB / ID: 3wdc
TitleN-terminal domain of Mycobacterium tuberculosis ClpC1 bound to Cyclomarin A
Components
  • Cyclomarin A
  • Probable ATP-dependent Clp protease ATP-binding subunit
KeywordsChaperone/Antimicrobial protein / Chaperone / Chaperone-Antimicrobial protein 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
Double Clp-N motif / Clp, N-terminal 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 / : ...Double Clp-N motif / Clp, N-terminal 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 / Clp repeat (R) domain profile. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclomarin A / ACETATE ION / ATP-dependent Clp protease ATP-binding subunit ClpC1 / ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Streptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsVasudevan, D. / Noble, C.G.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural basis of mycobacterial inhibition by cyclomarin A
Authors: Vasudevan, D. / Rao, S.P.S. / Noble, C.G.
History
DepositionJun 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent Clp protease ATP-binding subunit
B: Cyclomarin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1963
Polymers18,1372
Non-polymers591
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.880, 58.690, 63.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17073.557 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A522, UniProt: P9WPC9*PLUS
#2: Protein/peptide Cyclomarin A


Type: Cyclic peptide / Class: Antiinflammatory / Mass: 1063.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces (bacteria) / References: Cyclomarin A
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.74 Å3/Da / Density % sol: 29.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.2M ammonium acetate, 20% polyethylene glycol 3350, 0.025M magnesium, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→45 Å / Num. obs: 42423

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDB

3wdb


Resolution: 1.18→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.924 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1594 2141 5.1 %RANDOM
Rwork0.1223 ---
obs0.1241 40221 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.35 Å2 / Biso mean: 13.093 Å2 / Biso min: 3.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.18→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 4 167 1388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191516
X-RAY DIFFRACTIONr_angle_refined_deg1.9852.0242095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8115223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09423.42176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01715302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1871518
X-RAY DIFFRACTIONr_chiral_restr0.1030.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021162
X-RAY DIFFRACTIONr_rigid_bond_restr3.81131516
X-RAY DIFFRACTIONr_sphericity_free43.556523
X-RAY DIFFRACTIONr_sphericity_bonded12.2751600
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 152 -
Rwork0.166 2688 -
all-2840 -
obs--98.71 %

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