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- PDB-1do0: ORTHORHOMBIC CRYSTAL FORM OF HEAT SHOCK LOCUS U (HSLU) FROM ESCHE... -

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Basic information

Entry
Database: PDB / ID: 1do0
TitleORTHORHOMBIC CRYSTAL FORM OF HEAT SHOCK LOCUS U (HSLU) FROM ESCHERICHIA COLI
ComponentsPROTEIN (HEAT SHOCK LOCUS U)
KeywordsCHAPERONE / HSLU / CLPY / AAA-ATPASE / ATP-DEPENDENT PROTEOLYSIS / ATPASE / PROTEASOME
Function / homology
Function and homology information


protein denaturation / HslUV protease complex / proteasome-activating activity / protein unfolding / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding ...protein denaturation / HslUV protease complex / proteasome-activating activity / protein unfolding / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Heat shock protein HslU / : / Ubiquitin-associated (UBA) domain / 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 - #60 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) ...Heat shock protein HslU / : / Ubiquitin-associated (UBA) domain / 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 - #60 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / 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
ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent protease ATPase subunit HslU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D.
Citation
Journal: Nature / Year: 2000
Title: The structures of HsIU and the ATP-dependent protease HsIU-HsIV.
Authors: Bochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R.
#1: Journal: 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.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: HslV-HslU: A Novel ATP-Dependent Protease Complex in Escherichia coli Related to the Eukaryotic Proteasome
Authors: Rohrwild, M. / Coux, O. / Huang, H.C. / Moerschell, R.P. / Yoo, S.J. / Seol, J.H. / Chung, C.H. / Goldberg, A.L.
#3: Journal: Gene / Year: 1993
Title: Sequence Analysis of Four New Heat-Shock Genes Constituting the hslTS/ibpAB and hslVU Operons in Escherichia coli
Authors: Chuang, S.E. / Burland, V. / Plankett III, G. / Daniels, D.L. / Blattner, F.R.
History
DepositionDec 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HEAT SHOCK LOCUS U)
B: PROTEIN (HEAT SHOCK LOCUS U)
C: PROTEIN (HEAT SHOCK LOCUS U)
D: PROTEIN (HEAT SHOCK LOCUS U)
E: PROTEIN (HEAT SHOCK LOCUS U)
F: PROTEIN (HEAT SHOCK LOCUS U)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,44114
Polymers297,1716
Non-polymers2,2698
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29500 Å2
ΔGint-108 kcal/mol
Surface area109890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.15, 167.70, 108.19
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
PROTEIN (HEAT SHOCK LOCUS U)


Mass: 49528.508 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL-1 BLUE / Cellular location: CYTOPLASM / Plasmid: PET12B (T7 PROMOTOR) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6H5
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Sequence detailsEDMAN-DEGRADATION HAS SHOWN THAT THE AMINOTERMINAL METHIONINE IS CLEAVED IN THE WILD TYPE. ...EDMAN-DEGRADATION HAS SHOWN THAT THE AMINOTERMINAL METHIONINE IS CLEAVED IN THE WILD TYPE. NEVERTHELESS, THIS METHIONINE RESIDUE HAS BEEN ASSIGNED RESIDUE NUMBER 1. THE FOLLOWING SERINE, THE FIRST RESIDUE OF THE MATURE PROTEIN, HAS BEEN ASSIGNED RESIDUE NUMBER 2. AN ENGINEERED VARIANT OF HSLU WITH THE SEVEN RESIDUE HIS-TAG, MHHHHHH, IN PLACE OF MET1 HAS BEEN USED FOR CRYSTALLIZATION. THIS TAG IS NOT CLEAVED IN THE MUTANT PROTEIN. AS THESE RESIDUES ARE NOT VISIBLE IN THE ELECTRON DENSITY, THEY HAVE BEEN OMITTED FROM THE MODEL.

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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: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: reservoir: 100 mM sodium cacodylate, 15% glycerol, 10.5% PEG8000, 500 mM (NH4)2(SO4). drop: 0.002 ml protein (16mg/ml) in 20mM Tris/HCl pH 7.5, 1mM EDTA, 1mM NaN3, 0.002 ml reservoir, 0.0005 ...Details: reservoir: 100 mM sodium cacodylate, 15% glycerol, 10.5% PEG8000, 500 mM (NH4)2(SO4). drop: 0.002 ml protein (16mg/ml) in 20mM Tris/HCl pH 7.5, 1mM EDTA, 1mM NaN3, 0.002 ml reservoir, 0.0005 ml 1.0 M guanidinium chloride, 0.0005 ml C12E8 (octaethylene glycol monododecyl ether), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions in Buffer B
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
116 mg/mlprotein1drop
220 mMTris-HCl1dropBuffer B
31 mMEDTA1dropBuffer B
41 mM1dropBuffer BNaN3
5100 mMsodium cacodylate1reservoir
615 %glycerol1reservoir
710.5 %PEG80001reservoir
8500 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. all: 265668 / Num. obs: 74040 / % possible obs: 96.9 % / Redundancy: 3 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 7.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.526 / Rsym value: 52.6 / % possible all: 96
Reflection
*PLUS
Num. measured all: 265668
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HSLU FROM HSLU IN HSLVU CRYSTALS

Resolution: 3→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2596651.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.342 3765 5.1 %RANDOM
Rwork0.294 ---
obs0.294 73947 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.86 Å2 / ksol: 0.254 e/Å3
Displacement parametersBiso mean: 55.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.64 Å20 Å20 Å2
2--23.64 Å20 Å2
3----18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19230 0 136 0 19366
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.091.5
X-RAY DIFFRACTIONc_mcangle_it5.692
X-RAY DIFFRACTIONc_scbond_it10.512
X-RAY DIFFRACTIONc_scangle_it12.492.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.427 595 4.9 %
Rwork0.399 11466 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ATP.PARATP.TOP
X-RAY DIFFRACTION3SO4.PARSO4.TOP
X-RAY DIFFRACTION4PARAM19.IONMG.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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