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- PDB-1khy: The Crystal Structure of ClpB N Terminal Domain, Implication to t... -

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Basic information

Entry
Database: PDB / ID: 1khy
TitleThe Crystal Structure of ClpB N Terminal Domain, Implication to the Peptide Binding Function of ClpB
ComponentsCLPB PROTEIN
KeywordsCHAPERONE / alpha helix
Function / homology
Function and homology information


cellular response to heat / response to heat / protein refolding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component ...Double Clp-N motif / Clp, N-terminal domain / Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / 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 family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chaperone protein ClpB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJingzhi, L. / Bingdong, S.
CitationJournal: To be Published
Title: The Crystal Structure of E. coli Hsp100 ClpB N Terminal Domain, Implication to Peptide Binding Function of ClpB
Authors: Jingzhi, L. / Bingdong, S.
History
DepositionDec 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 21, 2021Group: Database references / Derived calculations / Refinement description
Category: refine / struct_conn / struct_ref_seq_dif
Item: _refine.ls_percent_reflns_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLPB PROTEIN
B: CLPB PROTEIN
C: CLPB PROTEIN
D: CLPB PROTEIN


Theoretical massNumber of molelcules
Total (without water)63,6784
Polymers63,6784
Non-polymers00
Water4,576254
1
A: CLPB PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,9191
Polymers15,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CLPB PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,9191
Polymers15,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CLPB PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,9191
Polymers15,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CLPB PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,9191
Polymers15,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.213, 52.600, 56.841
Angle α, β, γ (deg.)90.45, 111.73, 107.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CLPB PROTEIN / / HEAT SHOCK PROTEIN F84.1


Mass: 15919.484 Da / Num. of mol.: 4 / Fragment: N-terminal domain (residues 1-148)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpb / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63284
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 20K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.01, 0.9785, 0.9781, 0.9556
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(III) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.011
20.97851
30.97811
40.95561
ReflectionResolution: 1.95→30 Å / Num. all: 35923 / Num. obs: 35923 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.4
Reflection shellResolution: 1.95→2.04 Å / Redundancy: 2 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 11.2 / Rsym value: 0.128 / % possible all: 93.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.95→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3584 -random
Rwork0.222 ---
all0.226 35923 --
obs0.226 35923 90.6 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.18 Å21.66 Å2
2--1.34 Å22.28 Å2
3----1.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 0 254 4304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_dihedral_angle_d17.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.004
RfactorNum. reflection% reflection
Rfree0.259 3584 -
Rwork0.222 --
obs-35923 96.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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