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- PDB-4i81: Crystal Structure of ATPgS bound ClpX Hexamer -

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Basic information

Entry
Database: PDB / ID: 4i81
TitleCrystal Structure of ATPgS bound ClpX Hexamer
ComponentsATP-dependent Clp protease ATP-binding subunit ClpX
KeywordsMOTOR PROTEIN / ATPase / hexamer / ATPgS
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 / AAA domain (Cdc48 subfamily) ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-dependent Clp protease ATP-binding subunit ClpX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8182 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 1, 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)238,89412
Polymers236,6096
Non-polymers2,2856
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-135 kcal/mol
Surface area75360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.935, 199.167, 211.891
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: 39434.809 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-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
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: Jul 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. all: 24413 / Num. obs: 24413 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.8-3.876.50.843195.5
3.87-3.946.60.732198.6
3.94-4.016.60.529196.6
4.01-4.096.60.404196.1
4.09-4.186.80.358198.5
4.18-4.286.60.295199.9
4.28-4.396.60.261198.2
4.39-4.56.70.222199.2
4.5-4.646.70.185199.9
4.64-4.796.60.165198.8
4.79-4.966.80.173199.7
4.96-5.166.70.156199.1
5.16-5.396.70.148199.2
5.39-5.676.70.138199.7
5.67-6.036.80.131199.8
6.03-6.496.80.1071100
6.49-7.156.90.0811100
7.15-8.186.60.05199.8
8.18-10.296.70.0361100
10.29-506.20.032197.7

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Processing

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

3hws


Resolution: 3.8182→41.407 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.52 / σ(F): 0.12 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 1120 5 %
Rwork0.2707 --
obs0.2719 22386 90.56 %
all-21319 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 150 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-60.7594 Å2-0 Å2-0 Å2
2---41.4427 Å20 Å2
3----13.6863 Å2
Refinement stepCycle: LAST / Resolution: 3.8182→41.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12969 0 134 0 13103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613242
X-RAY DIFFRACTIONf_angle_d0.78317978
X-RAY DIFFRACTIONf_dihedral_angle_d13.1624851
X-RAY DIFFRACTIONf_chiral_restr0.1282230
X-RAY DIFFRACTIONf_plane_restr0.0022277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8182-3.99190.37121300.38952132X-RAY DIFFRACTION75
3.9919-4.20210.33891360.30932336X-RAY DIFFRACTION82
4.2021-4.46510.29061290.28762585X-RAY DIFFRACTION89
4.4651-4.80940.29261520.26372650X-RAY DIFFRACTION92
4.8094-5.29250.27011320.27962740X-RAY DIFFRACTION94
5.2925-6.05630.31091290.28842803X-RAY DIFFRACTION96
6.0563-7.62250.31951500.26752927X-RAY DIFFRACTION98
7.6225-41.40930.24521620.21563093X-RAY DIFFRACTION99

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