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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 / homologyClp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / ATPase family associated with various cellular activities (AAA) / P-loop containing nucleoside triphosphate hydrolase / AAA+ ATPase domain / ATPase, AAA-type, core / Heat shock protein HslU / peptidase activity, acting on L-amino acid peptides / HslUV protease complex ...Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / ATPase family associated with various cellular activities (AAA) / P-loop containing nucleoside triphosphate hydrolase / AAA+ ATPase domain / ATPase, AAA-type, core / Heat shock protein HslU / peptidase activity, acting on L-amino acid peptides / HslUV protease complex / protein hexamerization / protein unfolding / response to heat / ATPase activity / protein domain specific binding / proteolysis / magnesium ion binding / membrane / ATP binding / identical protein binding / cytosol / ATP-dependent protease ATPase subunit HslU
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 18, 1999 / Release: Feb 18, 2000
RevisionDateData content typeGroupProviderType
1.0Feb 18, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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
Polyers297,1716
Non-polymers2,2698
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)29500
ΔGint (kcal/M)-108
Surface area (Å2)109890
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 2

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Components

#1: Protein/peptide
PROTEIN (HEAT SHOCK LOCUS U)


Mass: 49528.508 Da / Num. of mol.: 6 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Strain: XL-1 BLUE / Cellular location: CYTOPLASM / Plasmid name: PET12B (T7 PROMOTOR) / Genus (production host): Escherichia / 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 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 96.063 Da / Num. of mol.: 2 / Formula: SO4 / Sulfate
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 / Density percent sol: 61.27 %
Crystal growTemp: 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 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

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
116 mg/mlproteindrop
220 mMTris-HCldropBuffer B
31 mMEDTAdropBuffer B
41 mMdropBuffer BNaN3
5100 mMsodium cacodylatereservoir
615 %glycerolreservoir
710.5 %PEG8000reservoir
8500 mMammonium sulfatereservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: MPG/DESY, HAMBURG BEAMLINE BW6 / Synchrotron site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Details: MIRROR / Detector: IMAGE PLATE / Collection date: Aug 15, 1999
RadiationMonochromator: DOUBLE CRYSTAL / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 55.1 Å2 / D resolution high: 3 Å / D resolution low: 35 Å / Number all: 265668 / Number obs: 74040 / Rmerge I obs: 0.079 / Rsym value: 7.9 / Redundancy: 3 % / Percent possible obs: 96.9
Reflection shellRmerge I obs: 0.526 / Highest resolution: 3 Å / Lowest resolution: 3.05 Å / Rsym value: 52.6 / Redundancy: 2.7 % / Percent possible all: 96
Reflection
*PLUS
Number measured all: 265668
Reflection shell
*PLUS
Percent possible obs: 96

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Processing

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

R Free selection details: RANDOM / Data cutoff high absF: 2596651.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 54.86 / Solvent model param ksol: 0.254
Displacement parametersB iso mean: 55.1 Å2 / Aniso B11: -5.64 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 23.64 Å2 / Aniso B23: 0 Å2 / Aniso B33: -18 Å2
Least-squares processR factor R free: 0.342 / R factor R free error: 0.006 / R factor R work: 0.294 / R factor obs: 0.294 / Highest resolution: 3 Å / Lowest resolution: 25 Å / Number reflection R free: 3765 / Number reflection obs: 73947 / Percent reflection R free: 5.1 / Percent reflection obs: 96.8
Refine analyzeLuzzati coordinate error free: 0.55 Å / Luzzati coordinate error obs: 0.46 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.61 Å / Luzzati sigma a obs: 0.54 Å
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 25 Å
Number of atoms included #LASTProtein: 19230 / Nucleic acid: 0 / Ligand: 136 / Solvent: 0 / Total: 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_it4.091.50
X-RAY DIFFRACTIONc_mcangle_it5.692.00
X-RAY DIFFRACTIONc_scbond_it10.512.00
X-RAY DIFFRACTIONc_scangle_it12.492.50
Refine LS shellHighest resolution: 3 Å / R factor R free: 0.427 / R factor R free error: 0.018 / R factor R work: 0.399 / Lowest resolution: 3.19 Å / Number reflection R free: 595 / Number reflection R work: 11466 / Total number of bins used: 6 / Percent reflection R free: 4.9 / Percent reflection 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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