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- PDB-3wdb: N-terminal domain of Mycobacterium tuberculosis ClpC1 -

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Basic information

Entry
Database: PDB / ID: 3wdb
TitleN-terminal domain of Mycobacterium tuberculosis ClpC1
ComponentsProbable ATP-dependent Clp protease ATP-binding subunit
KeywordsCHAPERONE
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 amino terminal domain, pathogenicity island component / : ...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 amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / 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
FORMIC ACID / ATP-dependent Clp protease ATP-binding subunit ClpC1 / ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4602
Polymers16,4141
Non-polymers461
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.370, 57.150, 65.020
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: 16413.855 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: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.2M ammonium acetate, 20% polyethylene glycol 3350, 0.025M magnesium formate, 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: 1.37→50 Å / Num. obs: 33696

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y1Q

2y1q


Resolution: 1.37→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.533 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 1709 5.1 %RANDOM
Rwork0.1434 ---
obs0.1455 31935 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.11 Å2 / Biso mean: 22.21 Å2 / Biso min: 7.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.57 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.37→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 3 170 1317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191246
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9871696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7423.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32415241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8311513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02944
X-RAY DIFFRACTIONr_rigid_bond_restr3.45131246
X-RAY DIFFRACTIONr_sphericity_free40.16552
X-RAY DIFFRACTIONr_sphericity_bonded18.79651339
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 106 -
Rwork0.316 2153 -
all-2259 -
obs--99.34 %

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