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- PDB-1ned: CRYSTAL STRUCTURE OF HSLV (CLPQ) AT 3.8 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ned
TitleCRYSTAL STRUCTURE OF HSLV (CLPQ) AT 3.8 ANGSTROMS RESOLUTION
ComponentsHSLVHslVU
KeywordsHYDROLASE / HSLV / CLPQ / HSLVU / CLPQY / ATP-DEPENDENT PROTEASE / PROTEASOME
Function / homology
Function and homology information


HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding ...HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding / proteolysis / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP-dependent protease, HslV subunit / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3.8 Å
AuthorsBochtler, M. / Ditzel, L. / Groll, M. / Huber, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal structure of heat shock locus V (HslV) from Escherichia coli.
Authors: Bochtler, M. / Ditzel, L. / Groll, M. / Huber, R.
History
DepositionApr 4, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HSLV
B: HSLV
C: HSLV


Theoretical massNumber of molelcules
Total (without water)60,2753
Polymers60,2753
Non-polymers00
Water0
1
A: HSLV
B: HSLV
C: HSLV

A: HSLV
B: HSLV
C: HSLV

A: HSLV
B: HSLV
C: HSLV

A: HSLV
B: HSLV
C: HSLV


Theoretical massNumber of molelcules
Total (without water)241,10212
Polymers241,10212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)108.400, 108.400, 103.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein HSLV / HslVU


Mass: 20091.811 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL-1 BLUE / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7B8, EC: 3.4.99.-

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5
Details: 100MM HEPES/NAOH PH 7.5 200MM SODIUM ACETATE 0.02 % SODIUM AZIDE 9-14% ETHANOL
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMHEPES-NaOH1reservoirpH7.5
2200 mMsodium acetate1reservoir
30.02 %1reservoirNaN3
49-14 %ethanol1reservoir
510 mg/mlprotain1drop
620 mMTris-HCl1drop
7300 mM1dropNaCl
81 mMEDTA1drop
91 mM1dropNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.8→15 Å / Num. obs: 6404 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rsym value: 0.073
Reflection shellResolution: 3.8→3.93 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.205 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 36796 / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
CCP4model building
FRODOmodel building
X-PLOR3.842refinement
MOSFLMV. 5.3data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 3.8→15 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.315 -2 %
Rwork0.256 --
obs0.256 6035 99.4 %
Displacement parametersBiso mean: 51.7 Å2
Refinement stepCycle: LAST / Resolution: 3.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4055 0 0 0 4055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.9
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSRms dev Biso : 3.5 Å2 / Rms dev position: 0.06 Å
Software
*PLUS
Name: X-PLOR / Version: 3.842 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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