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- PDB-4i34: Crystal Structure of W-W-W ClpX Hexamer -

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Basic information

Entry
Database: PDB / ID: 4i34
TitleCrystal Structure of W-W-W ClpX Hexamer
ComponentsATP-dependent Clp protease ATP-binding subunit ClpX
KeywordsMOTOR PROTEIN / ATPase / hexamer / asymmetric
Function / homology
Function and homology information


protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protease binding ...protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protease binding / protein dimerization activity / cell division / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Clp protease, ATP-binding subunit ClpX, bacteria / Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / ClpX C4-type zinc finger / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein ...Clp protease, ATP-binding subunit ClpX, bacteria / Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / ClpX C4-type zinc finger / 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, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent Clp protease ATP-binding subunit ClpX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.1218 Å
AuthorsGlynn, S.E. / Nager, A.R. / Stinson, B.S. / Schmitz, K.R. / Baker, T.A. / Sauer, R.T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Nucleotide Binding and Conformational Switching in the Hexameric Ring of a AAA+ Machine.
Authors: Stinson, B.M. / Nager, A.R. / Glynn, S.E. / Schmitz, K.R. / Baker, T.A. / Sauer, R.T.
History
DepositionNov 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Refinement description
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpX
B: ATP-dependent Clp protease ATP-binding subunit ClpX
C: ATP-dependent Clp protease ATP-binding subunit ClpX
D: ATP-dependent Clp protease ATP-binding subunit ClpX
E: ATP-dependent Clp protease ATP-binding subunit ClpX
F: ATP-dependent Clp protease ATP-binding subunit ClpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,19112
Polymers236,6156
Non-polymers5766
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16620 Å2
ΔGint-201 kcal/mol
Surface area76880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.341, 199.606, 203.441
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
ATP-dependent Clp protease ATP-binding subunit ClpX


Mass: 39435.793 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0438, clpX, JW0428, lopC / Plasmid: pACYC / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: P0A6H1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4

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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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.8
Details: 75 mM sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.1218→50 Å / Num. all: 18530 / Num. obs: 18530 / % possible obs: 97.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
4.1218-4.34.30.294184.1
4.3-4.474.90.258192.6
4.47-4.675.50.207197.8
4.67-4.925.80.185199.2
4.92-5.236.20.16199.9
5.23-5.636.30.148199.9
5.63-6.26.30.118199.9
6.2-7.096.20.0851100
7.09-8.9360.056199.8
8.93-505.60.034198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HWS

3hws


Resolution: 4.1218→38.337 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.53 / σ(F): 1.34 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3077 945 5.12 %
Rwork0.2744 --
obs0.2761 18471 96.55 %
all-18471 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 156.776 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-44.344 Å2-0 Å20 Å2
2---53.3418 Å2-0 Å2
3---8.9978 Å2
Refinement stepCycle: LAST / Resolution: 4.1218→38.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13785 0 30 0 13815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313958
X-RAY DIFFRACTIONf_angle_d0.49918911
X-RAY DIFFRACTIONf_dihedral_angle_d10.5645068
X-RAY DIFFRACTIONf_chiral_restr0.0332309
X-RAY DIFFRACTIONf_plane_restr0.0022430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1218-4.33890.35721080.34462084X-RAY DIFFRACTION82
4.3389-4.61030.3351410.31622406X-RAY DIFFRACTION96
4.6103-4.96560.30351520.29782522X-RAY DIFFRACTION99
4.9656-5.4640.33171520.31312542X-RAY DIFFRACTION100
5.464-6.25170.37851420.33172585X-RAY DIFFRACTION100
6.2517-7.86530.33391100.27282646X-RAY DIFFRACTION100
7.8653-38.33910.24131400.21592741X-RAY DIFFRACTION99
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)
11.2845-0.611.11124.4230.07314.78970.29960.19350.4095-0.4703-0.03050.21570.3657-0.1812-0.20941.6847-0.0356-0.14391.88040.09561.692519.6097-68.4648-16.7407
22.0213-1.17-2.77265.14681.08196.5748-0.11230.3399-0.22410.03620.1439-0.40150.1623-0.0422-0.04391.6544-0.0144-0.25651.9369-0.17131.85346.3986-51.947-41.2371
35.6699-2.2079-1.38460.87870.13314.00060.05810.02310.2304-0.5244-0.10330.29020.03490.0599-0.022.20510.0718-0.45751.6973-0.07922.0952-5.5603-67.6632-65.7476
42.3996-0.53580.2328-0.2362-0.1523.84420.0203-0.2888-0.21280.312-0.32410.2517-0.48070.16280.16332.6382-0.1-0.12962.41260.16232.7156-5.3565-102.8252-48.1625
54.85461.31594.02693.51825.31169.42650.92581.1255-0.598-0.12490.2567-0.3232-0.70860.4231-0.66742.6256-0.181-0.2542.7977-0.25212.4935-4.7762-117.2447-19.0452
65.85461.3009-2.61396.5695-0.77744.57790.0240.3011-0.2192-0.3005-0.40550.190.7915-0.520.20562.1874-0.27550.06522.21630.00962.155912.8428-101.95122.6497
70.116-1.35060.68733.72890.52336.33130.3913-0.54320.4259-0.56440.067-0.39790.27470.0501-0.24531.8365-0.15150.17562.0188-0.10441.926610.564-35.9431-25.1692
84.7114-3.26272.11142.97671.01883.76030.4167-0.283-0.4197-0.2316-0.2535-0.856-0.2273-0.21790.10761.9631-0.006-0.09891.8385-0.03422.1165-18.8341-48.7305-63.7674
93.02431.85650.91392.74910.91753.06250.27850.12260.7301-0.6771-0.59591.3784-0.30180.10860.44872.0930.0915-0.21552.099-0.23622.5845-9.391-100.2806-70.2691
101.7101-0.1911.68261.5432-0.99983.18721.39690.191-0.9099-0.3141-0.05130.7909-0.27471.1297-0.80742.61490.3431-0.63522.7343-0.39772.5521-20.5782-128.8043-31.0894
111.9474-0.4439-1.49420.06110.2373.3103-0.27-0.1882-0.96970.85050.02820.1687-0.04260.00870.36972.8488-0.43770.3062.33190.00832.6345-4.3803-112.890714.4142
123.89682.37022.03134.23021.62713.78430.02560.72450.68480.33060.2828-0.05540.56090.2089-0.37491.53780.11730.07541.68310.08281.522628.1901-72.64364.6212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 63:318 or resid 501)
2X-RAY DIFFRACTION2chain B and (resid 64:318 or resid 501)
3X-RAY DIFFRACTION3chain C and (resid 63:318 or resid 501)
4X-RAY DIFFRACTION4chain D and (resid 63:318 or resid 501)
5X-RAY DIFFRACTION5chain E and (resid 64:318 or resid 501)
6X-RAY DIFFRACTION6chain F and (resid 63:318 or resid 501)
7X-RAY DIFFRACTION7chain A and resid 319:413
8X-RAY DIFFRACTION8chain B and resid 319:413
9X-RAY DIFFRACTION9chain C and resid 319:413
10X-RAY DIFFRACTION10chain D and resid 319:413
11X-RAY DIFFRACTION11chain E and resid 319:413
12X-RAY DIFFRACTION12chain F and resid 319:413

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