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- PDB-3fes: Crystal Structure of the ATP-dependent Clp Protease ClpC from Clo... -

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Basic information

Entry
Database: PDB / ID: 3fes
TitleCrystal Structure of the ATP-dependent Clp Protease ClpC from Clostridium difficile
ComponentsATP-dependent Clp endopeptidase
KeywordsATP binding protein / alpha-helical bundles / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Chaperone / Nucleotide-binding / Protease
Function / homology
Function and homology information


Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain ...Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / 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, 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
Class III stress response-related ATPase, AAA+ superfamily
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsKim, Y. / Tesar, C. / Li, H. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the ATP-dependent Clp Protease ClpC from Clostridium difficile
Authors: Kim, Y. / Tesar, C. / Li, H. / Cobb, G. / Joachimiak, A.
History
DepositionDec 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: ATP-dependent Clp endopeptidase
B: ATP-dependent Clp endopeptidase
C: ATP-dependent Clp endopeptidase
D: ATP-dependent Clp endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,33113
Polymers64,2194
Non-polymers1,1129
Water4,774265
1
A: ATP-dependent Clp endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0792
Polymers16,0551
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-dependent Clp endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2733
Polymers16,0551
Non-polymers2192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP-dependent Clp endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7065
Polymers16,0551
Non-polymers6514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ATP-dependent Clp endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2733
Polymers16,0551
Non-polymers2192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.690, 68.523, 81.339
Angle α, β, γ (deg.)66.91, 86.23, 85.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
ATP-dependent Clp endopeptidase / ATP-dependent Clp protease


Mass: 16054.753 Da / Num. of mol.: 4 / Fragment: residues 2-143, ATP-binding
Source method: isolated from a genetically manipulated source
Details: N-terminal maltose-binding protein fusion which is cleaved before purification and a 6-His tag with a TEV protease cut site.
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD0026, clpC, mecB / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q18CA9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M MgCl2, 0.1 M Citrate pH 5.5, 40% (v/v) PEG-400, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.82→34.55 Å / Num. all: 59636 / Num. obs: 59636 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.1
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2970 / % possible all: 95.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0053refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→34.55 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.491 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3015 5.1 %RANDOM
Rwork0.187 ---
all0.189 56400 --
obs0.189 56400 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å21.21 Å20.65 Å2
2---0.49 Å2-1.4 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.82→34.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 71 265 4690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9896196
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3025592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70725.517203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17115897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0051523
X-RAY DIFFRACTIONr_chiral_restr0.1140.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9211.52866
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72924590
X-RAY DIFFRACTIONr_scbond_it3.04831754
X-RAY DIFFRACTIONr_scangle_it5.1044.51606
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 226 -
Rwork0.275 4105 -
obs-4331 95.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3744-0.3025-0.21042.03990.65752.43820.0090.0360.0277-0.0538-0.0451-0.012-0.108-0.05140.03610.0166-0.01490.01110.10740.0130.027917.285556.650744.8236
21.3955-0.4916-0.35152.4137-0.06911.0395-0.01850.0351-0.04-0.07820.0016-0.03390.0197-0.08870.01690.0086-0.0093-0.01230.03140.00730.05849.919186.638572.5418
30.9137-0.5225-0.23763.6439-0.8751.5704-0.1098-0.10360.00880.29990.0892-0.1236-0.12240.08220.02060.03630.0063-0.00190.0636-0.00060.066720.566349.01174.226
41.0519-0.42290.23971.55940.59423.8527-0.0167-0.0786-0.1190.04780.03320.13320.46250.0495-0.01640.06220.00590.0070.06540.00490.03336.979167.784496.5029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 142
2X-RAY DIFFRACTION2B1 - 141
3X-RAY DIFFRACTION3C1 - 142
4X-RAY DIFFRACTION4D1 - 142

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