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- PDB-2ds8: Structure of the ZBD-XB complex -

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Basic information

Entry
Database: PDB / ID: 2ds8
TitleStructure of the ZBD-XB complex
Components
  • ATP-dependent Clp protease ATP-binding subunit clpX
  • SspB-tail peptide
KeywordsMETAL BINDING PROTEIN / PROTEIN BINDING / Protein-peptide complex
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
ClpX chaperone, C4-type zinc finger domain / Erythroid Transcription Factor GATA-1; Chain A / 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 ...ClpX chaperone, C4-type zinc finger domain / Erythroid Transcription Factor GATA-1; Chain A / 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 / Other non-globular / ATPase, AAA-type, core / Special / 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: 1.6 Å
AuthorsPark, E.Y. / Lee, B.G. / Hong, S.B. / Kim, H.W. / Song, H.K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Basis of SspB-tail Recognition by the Zinc Binding Domain of ClpX.
Authors: Park, E.Y. / Lee, B.G. / Hong, S.B. / Kim, H.W. / Jeon, H. / Song, H.K.
History
DepositionJun 22, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit clpX
P: SspB-tail peptide
B: ATP-dependent Clp protease ATP-binding subunit clpX
Q: SspB-tail peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3586
Polymers13,2274
Non-polymers1312
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-31 kcal/mol
Surface area5850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.554, 46.548, 57.037
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 / ClpX


Mass: 5758.631 Da / Num. of mol.: 2 / Fragment: Zinc binding domain(ZBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6H1
#2: Protein/peptide SspB-tail peptide / XB


Mass: 855.079 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: XB peptide (APALRVVK) is synthesized. Except the first alanine, the sequence occurs naturally in E. coli SspB
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.633 Å3/Da / Density % sol: 24.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M tri-sodium citrate, pH 6.5, 10-fold molar excess of XB peptide addition, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2005
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 11450 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.66 Å / % possible all: 64.1

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DS5

2ds5


Resolution: 1.6→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2256 1126 Random
Rwork0.201 --
all0.2025 11956 -
obs0.201 10887 -
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 0 2 86 833
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003508
X-RAY DIFFRACTIONc_angle_deg1.08774
LS refinement shellResolution: 1.6→1.63 Å / Rfactor Rfree error: 0.0124
RfactorNum. reflection
Rfree0.3091 25
Rwork0.2967 -
obs-276

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