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- PDB-4i9k: Crystal structure of symmetric W-W-W ClpX Hexamer -

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Basic information

Entry
Database: PDB / ID: 4i9k
TitleCrystal structure of symmetric W-W-W ClpX Hexamer
ComponentsATP-dependent Clp protease ATP-binding subunit ClpX
KeywordsMOTOR PROTEIN / ATPase / symmetric / hexamer
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
Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / : / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein ...Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / : / 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, 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 / Resolution: 5.0003 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
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2566
Polymers78,8722
Non-polymers3844
Water00
1
A: ATP-dependent Clp protease ATP-binding subunit ClpX
B: ATP-dependent Clp protease ATP-binding subunit ClpX
hetero molecules

A: ATP-dependent Clp protease ATP-binding subunit ClpX
B: ATP-dependent Clp protease ATP-binding subunit ClpX
hetero molecules

A: ATP-dependent Clp protease ATP-binding subunit ClpX
B: ATP-dependent Clp protease ATP-binding subunit ClpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,76818
Polymers236,6156
Non-polymers1,15312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area14070 Å2
ΔGint-90 kcal/mol
Surface area72930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.430, 119.430, 111.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 39435.793 Da / Num. of mol.: 2
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


Mass: 96.063 Da / Num. of mol.: 4 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 2 M ammonium sulfate, 0.15 M potassium sulfate, 4 mM ATP, 4 mM magnesium sulfate, 50 mM EDTA, pH 7.5, 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: Jun 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.506→59.715 Å / Num. all: 5160 / Num. obs: 5160 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rsym value: 0.186 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
4.506-4.756.60.2722.150627700.27295.7
4.75-5.046.50.308245827040.30895.3
5.04-5.396.50.2982.243746680.29895.1
5.39-5.826.50.2562.340086190.25694.8
5.82-6.376.50.2632.536965720.26394.8
6.37-7.126.40.2122.633945310.21294.6
7.12-8.236.20.1653.127584460.16594.5
8.23-10.0860.1463.522803820.14692.1
10.08-14.256.80.143.320012960.1493.5
14.25-59.7155.90.1442.610191720.14491.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HWS

3hws


Resolution: 5.0003→49.15 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5862 / SU ML: 0.75 / Phase error: 44.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3544 353 9.48 %RANDOM
Rwork0.3163 ---
all0.3196 3723 --
obs0.3196 3723 93.36 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 188.461 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 290.44 Å2 / Biso mean: 240.9206 Å2 / Biso min: 194.68 Å2
Baniso -1Baniso -2Baniso -3
1--115.3428 Å20 Å20 Å2
2---115.3428 Å2-0 Å2
3---219.9114 Å2
Refinement stepCycle: LAST / Resolution: 5.0003→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4394 0 20 0 4414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024454
X-RAY DIFFRACTIONf_angle_d0.4686036
X-RAY DIFFRACTIONf_chiral_restr0.03744
X-RAY DIFFRACTIONf_plane_restr0.002770
X-RAY DIFFRACTIONf_dihedral_angle_d12.7011606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
5.0003-5.72290.39521210.41231126124794
5.7229-7.20660.43371250.36531104122994
7.2066-49.15230.30421070.25951140124792

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