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- PDB-4i4l: Crystal Structure of Nucleotide-Bound W-W-W ClpX Hexamer -

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Basic information

Entry
Database: PDB / ID: 4i4l
TitleCrystal Structure of Nucleotide-Bound W-W-W ClpX Hexamer
ComponentsATP-dependent Clp protease ATP-binding subunit ClpX
KeywordsMOTOR PROTEIN / hexamer / wild-type / asymmetric / nucleotide-bound
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. / : / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal ...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. / : / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Helicase, Ruva Protein; domain 3 / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 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: 3.6981 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 27, 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
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)237,61813
Polymers236,6156
Non-polymers1,0047
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-191 kcal/mol
Surface area77810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.942, 181.903, 201.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (backbone or name CB) and (resid 67:97...
21chain B and (backbone or name CB) and (resid 67:97...
31chain C and (backbone or name CB) and (resid 67:97...
41chain D and (backbone or name CB) and (resid 67:97...
51chain E and (backbone or name CB) and (resid 67:97...
61chain F and (backbone or name CB) and (resid 67:97...
12chain A and (backbone or name CB) and (resid 319:412)
22chain B and (backbone or name CB) and (resid 319:412)
32chain C and (backbone or name CB) and (resid 319:412)
42chain D and (backbone or name CB) and (resid 319:412)
52chain E and (backbone or name CB) and (resid 319:412)
62chain F and (backbone or name CB) and (resid 319:412)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (backbone or name CB) and (resid 67:97...A63 - 413
121chain A and (backbone or name CB) and (resid 67:97...A63 - 413
211chain B and (backbone or name CB) and (resid 67:97...B63 - 413
221chain B and (backbone or name CB) and (resid 67:97...B63 - 413
311chain C and (backbone or name CB) and (resid 67:97...C63 - 413
321chain C and (backbone or name CB) and (resid 67:97...C63 - 413
411chain D and (backbone or name CB) and (resid 67:97...D63 - 413
421chain D and (backbone or name CB) and (resid 67:97...D63 - 413
511chain E and (backbone or name CB) and (resid 67:97...E63 - 413
521chain E and (backbone or name CB) and (resid 67:97...E63 - 413
611chain F and (backbone or name CB) and (resid 67:97...F63 - 413
621chain F and (backbone or name CB) and (resid 67:97...F63 - 413
112chain A and (backbone or name CB) and (resid 319:412)A0
212chain B and (backbone or name CB) and (resid 319:412)B0
312chain C and (backbone or name CB) and (resid 319:412)C0
412chain D and (backbone or name CB) and (resid 319:412)D0
512chain E and (backbone or name CB) and (resid 319:412)E0
612chain F and (backbone or name CB) and (resid 319:412)F0

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.624283, 0.691705, 0.363064), (-0.743743, 0.384082, 0.547108), (0.238991, -0.611576, 0.754227)39.561298, 22.5156, -14.8208
2given(0.147847, 0.484668, 0.862112), (-0.630522, -0.625384, 0.459714), (0.76196, -0.611548, 0.213133)68.348503, 1.68583, -38.103298
3given(0.630884, -0.655441, 0.41519), (-0.582207, -0.753638, -0.305066), (0.512856, -0.049265, -0.85706)7.13153, -21.0375, -69.477997
4given(-0.122464, -0.979217, -0.161665), (-0.379664, 0.196724, -0.903966), (0.916983, -0.049325, -0.395865)21.937201, -31.5993, -54.330799
5given(0.193832, -0.662336, -0.723699), (0.358703, 0.734458, -0.57611), (0.913105, -0.147925, 0.379943)6.03775, -34.139599, -31.163
6given(0.745528, 0.63338, 0.207407), (-0.577704, 0.458961, 0.674991), (0.332334, -0.623044, 0.708075)25.1187, 27.430599, -21.340599
7given(0.947725, 0.229153, 0.222049), (-0.005581, -0.683876, 0.729577), (0.319039, -0.692678, -0.646847)-6.36112, -6.10718, -76.491798
8given(0.40517, -0.785339, 0.46806), (-0.818363, -0.539782, -0.197275), (0.407579, -0.303113, -0.861396)22.2691, -7.88687, -63.2104
9given(0.03237, -0.990434, 0.13414), (-0.23972, -0.137986, -0.960986), (0.970302, -0.001049, -0.241893)16.6891, -35.186901, -55.977299
10given(0.510868, -0.798015, 0.319666), (0.786712, 0.284089, -0.548068), (0.346553, 0.531475, 0.772939)-7.20925, -47.18, -16.23

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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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


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: 2.17 Å3/Da / Density % sol: 43.19 %
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: 3.698→50 Å / Num. all: 21372 / Num. obs: 21372 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Χ2: 1.023 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.698-3.833.40.30920980.56195.3
3.83-3.993.80.26921310.754194.9
3.99-4.173.90.19421370.768196.9
4.17-4.393.90.16521091.037193.5
4.39-4.6640.11821480.926194.6
4.66-5.023.90.10121460.955195.5
5.02-5.5340.121270.905194
5.53-6.3240.08821220.902192.5
6.32-7.963.90.06421501.423192
7.96-503.60.03722041.976189.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
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: 3.6981→45.476 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7302 / SU ML: 0.59 / σ(F): 0.11 / Phase error: 32.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3227 1026 5.02 %RANDOM
Rwork0.2997 ---
all0.3009 20446 --
obs0.3009 20446 89.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.102 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 475.11 Å2 / Biso mean: 145.9978 Å2 / Biso min: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.8875 Å20 Å2-0 Å2
2--4.54 Å20 Å2
3----0.6525 Å2
Refinement stepCycle: LAST / Resolution: 3.6981→45.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13647 0 57 0 13704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213842
X-RAY DIFFRACTIONf_angle_d0.43918745
X-RAY DIFFRACTIONf_chiral_restr0.0282291
X-RAY DIFFRACTIONf_plane_restr0.0022393
X-RAY DIFFRACTIONf_dihedral_angle_d9.9395009
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A655X-RAY DIFFRACTIONPOSITIONAL0.009
12B655X-RAY DIFFRACTIONPOSITIONAL0.009
13C655X-RAY DIFFRACTIONPOSITIONAL0.01
14D655X-RAY DIFFRACTIONPOSITIONAL0.008
15E511X-RAY DIFFRACTIONPOSITIONAL0.01
16F655X-RAY DIFFRACTIONPOSITIONAL0.01
21A466X-RAY DIFFRACTIONPOSITIONAL0.113
22B466X-RAY DIFFRACTIONPOSITIONAL0.113
23C466X-RAY DIFFRACTIONPOSITIONAL0.138
24D466X-RAY DIFFRACTIONPOSITIONAL0.107
25E466X-RAY DIFFRACTIONPOSITIONAL0.134
26F466X-RAY DIFFRACTIONPOSITIONAL0.139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6981-3.8930.36091270.35632507263483
3.893-4.13680.38421500.3332698284889
4.1368-4.45590.32071450.30712754289990
4.4559-4.90390.33761480.2952809295792
4.9039-5.61230.33261650.32022826299191
5.6123-7.06670.35311300.32862869299991
7.0667-45.47920.2551610.24112957311890

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