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- PDB-3hws: Crystal structure of nucleotide-bound hexameric ClpX -

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Basic information

Entry
Database: PDB / ID: 3hws
TitleCrystal structure of nucleotide-bound hexameric ClpX
ComponentsATP-dependent Clp protease ATP-binding subunit clpX
KeywordsMOTOR PROTEIN / ClpXP / AAA+ molecular machine / hexamer / asymmetric / ATP-binding / Chaperone / Metal-binding / Nucleotide-binding / Stress response / Zinc-finger / METAL BINDING PROTEIN
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 / : / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal ...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 / : / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / 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 / Resolution: 3.25 Å
AuthorsGlynn, S.E. / Martin, A. / Baker, T.A. / Sauer, R.T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine.
Authors: Glynn, S.E. / Martin, A. / Nager, A.R. / Baker, T.A. / Sauer, R.T.
History
DepositionJun 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)239,61525
Polymers236,6096
Non-polymers3,00619
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 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)119,5439
Polymers118,3043
Non-polymers1,2396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-94 kcal/mol
Surface area43720 Å2
MethodPISA
3
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,07216
Polymers118,3043
Non-polymers1,76813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-156 kcal/mol
Surface area42690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.085, 178.498, 201.369
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
11B
21A
31C
41D
51E
61F
12B
22A
32C
42D
52E
62F

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

NCS ensembles :
ID
1
2

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Components

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


Mass: 39434.809 Da / Num. of mol.: 6 / Fragment: covalently linked ClpX lacking N-terminal domain / Mutation: E185Q, K408E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / 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.: 4 / 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.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Sodium acetate, ammonium sulfate Soaked overnight in mother liquor plus 5 mM ATP-G-S / 5 mM magnesium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, 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: Oct 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 32170 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.061 / Χ2: 1 / Net I/σ(I): 23.694
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.25-3.3760.57131800.8271100
3.37-3.560.36831330.894199.9
3.5-3.6660.22131830.888199.8
3.66-3.8560.14931930.941100
3.85-4.0960.10231660.964199.8
4.09-4.4160.07132040.995199.8
4.41-4.8560.05832211.002199.7
4.85-5.565.90.05832181.088199.3
5.56-75.80.06232591.319199.3
7-505.50.03734131.098198

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→45.081 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.772 / SU ML: 0.42 / σ(F): 0.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 1497 4.91 %
Rwork0.243 --
obs0.245 30512 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 104.446 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 460.31 Å2 / Biso mean: 142.033 Å2 / Biso min: 51.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.25→45.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14112 0 175 5 14292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314446
X-RAY DIFFRACTIONf_angle_d0.68719603
X-RAY DIFFRACTIONf_chiral_restr0.042370
X-RAY DIFFRACTIONf_plane_restr0.0022502
X-RAY DIFFRACTIONf_dihedral_angle_d13.4655213
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B655X-RAY DIFFRACTIONPOSITIONAL0.215
12A655X-RAY DIFFRACTIONPOSITIONAL0.215
13C655X-RAY DIFFRACTIONPOSITIONAL0.271
14D655X-RAY DIFFRACTIONPOSITIONAL0.229
15E580X-RAY DIFFRACTIONPOSITIONAL0.215
16F655X-RAY DIFFRACTIONPOSITIONAL0.302
21B466X-RAY DIFFRACTIONPOSITIONAL0.267
22A466X-RAY DIFFRACTIONPOSITIONAL0.267
23C466X-RAY DIFFRACTIONPOSITIONAL0.297
24D466X-RAY DIFFRACTIONPOSITIONAL0.221
25E466X-RAY DIFFRACTIONPOSITIONAL0.23
26F466X-RAY DIFFRACTIONPOSITIONAL0.275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.25-3.3550.4061060.3142418252489
3.355-3.4750.3291360.282438257491
3.475-3.6140.3021260.2582587271395
3.614-3.7780.31230.2472569269296
3.778-3.9770.2971470.2382614276197
3.977-4.2260.2871330.2282664279798
4.226-4.5520.2971500.2162677282798
4.552-5.010.2131520.2152675282799
5.01-5.7340.3081340.2432724285899
5.734-7.2190.31440.2622768291299
7.219-45.0850.2351460.2192881302798

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