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- PDB-2ds7: Structure of the ZBD in the hexagonal crystal form -

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Basic information

Entry
Database: PDB / ID: 2ds7
TitleStructure of the ZBD in the hexagonal crystal form
ComponentsATP-dependent Clp protease ATP-binding subunit clpX
KeywordsMETAL BINDING PROTEIN / PROTEIN BINDING / C43M mutant / zinc binding domain of ClpX / selenomethionine incorporation
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 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein ...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 / 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 / MAD / Resolution: 2.5 Å
AuthorsPark, E.Y. / Lee, B.G. / Hong, S.B. / 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 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit clpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8992
Polymers5,8341
Non-polymers651
Water1267
1
A: ATP-dependent Clp protease ATP-binding subunit clpX
hetero molecules

A: ATP-dependent Clp protease ATP-binding subunit clpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7984
Polymers11,6672
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)41.053, 41.053, 102.234
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 5833.579 Da / Num. of mol.: 1 / Fragment: Zinc binding domain(ZBD) / Mutation: C43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P0A6H1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM sodium acetate, pH 4.6, 200mM lithium sulfate, 12% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.95, 0.97924, 0.97868
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.979241
30.978681
ReflectionResolution: 2.5→30 Å / Num. obs: 2074 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.59 Å / % possible all: 98

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2723 329 RANDOM
Rwork0.235 --
all0.2394 --
obs0.235 2009 -
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms291 0 1 7 299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005619
X-RAY DIFFRACTIONc_angle_deg1.10366
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.0506
RfactorNum. reflection
Rfree0.3411 31
Rwork0.2905 -
obs-369

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