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- PDB-1g3i: CRYSTAL STRUCTURE OF THE HSLUV PROTEASE-CHAPERONE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1g3i
TitleCRYSTAL STRUCTURE OF THE HSLUV PROTEASE-CHAPERONE COMPLEX
Components
  • ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
  • ATP-DEPENDENT PROTEASE HSLV
KeywordsCHAPERONE/HYDROLASE / CHAPERONE-HYDROLASE complex
Function / homologyHeat shock protein HslU / Clp ATPase, C-terminal / Proteasome beta-type subunit profile. / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Proteasome subunit / ATPase family associated with various cellular activities (AAA) / Nucleophile aminohydrolases, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Proteasome B-type subunit ...Heat shock protein HslU / Clp ATPase, C-terminal / Proteasome beta-type subunit profile. / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Proteasome subunit / ATPase family associated with various cellular activities (AAA) / Nucleophile aminohydrolases, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Proteasome B-type subunit / Proteasome, subunit alpha/beta / AAA+ ATPase domain / ATPase, AAA-type, core / ATP-dependent protease, HslV subunit / HslU-HslV peptidase / peptidase activity, acting on L-amino acid peptides / HslUV protease complex / protein unfolding / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in cellular protein catabolic process / ATPase activity / ATP binding / metal ion binding / ATP-dependent protease subunit HslV / ATP-dependent protease ATPase subunit HslU
Function and homology information
Specimen sourceHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.41 Å resolution
AuthorsSousa, M.C. / Trame, C.B. / Tsuruta, H. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal and solution structures of an HslUV protease-chaperone complex.
Authors: Sousa, M.C. / Trame, C.B. / Tsuruta, H. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 24, 2000 / Release: Nov 22, 2000
RevisionDateData content typeGroupProviderType
1.0Nov 22, 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: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
B: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
C: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
D: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
E: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
G: ATP-DEPENDENT PROTEASE HSLV
H: ATP-DEPENDENT PROTEASE HSLV
I: ATP-DEPENDENT PROTEASE HSLV
J: ATP-DEPENDENT PROTEASE HSLV
K: ATP-DEPENDENT PROTEASE HSLV
L: ATP-DEPENDENT PROTEASE HSLV
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV
Q: ATP-DEPENDENT PROTEASE HSLV
R: ATP-DEPENDENT PROTEASE HSLV
S: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
T: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
U: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
V: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
W: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
X: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)826,22736
Polyers820,14124
Non-polymers6,08612
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)92590
ΔGint (kcal/M)-248
Surface area (Å2)232070
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)209.223, 220.579, 241.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2
DetailsThe biological assembly is the complex HslU12-HslV12 seen in the asymmetric unit.

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Components

#1: Protein/peptide
ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU / HSLU


Mass: 49441.504 Da / Num. of mol.: 12 / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Genus: Haemophilus / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43773
#2: Protein/peptide
ATP-DEPENDENT PROTEASE HSLV / HSLV


Mass: 18903.549 Da / Num. of mol.: 12 / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Genus: Haemophilus / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P43772, Hydrolases, Acting on peptide bonds (peptidases), Endopeptidases of unknown catalytic mechanism (sub-subclass is currently empty)
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

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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: 3.39 / Density percent sol: 63.72 %
Crystal growTemp: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG monomethyl ether 2000, potassium Chloride, magnesium acetate, citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 7
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
15-20 mg/mlprotein1drop
210 mMMOPS1drop
31 mM1dropMg(OAc)2
41 mMATP1drop
53-6 %PEG2000MME1reservoir
61 M1reservoirKCl
710 mM1reservoirMg(OAc)2
850 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 5.0.2 / Synchrotron site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Jun 23, 2000
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionD resolution high: 3.4 Å / D resolution low: 30 Å / Number all: 134912 / Number obs: 134912 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.064 / NetI over sigmaI: 11.5 / Redundancy: 2.2 % / Percent possible obs: 89.1
Reflection shellRmerge I obs: 0.285 / Highest resolution: 3.4 Å / Lowest resolution: 3.52 Å / MeanI over sigI obs: 3 / Redundancy: 1.8 % / Percent possible all: 80.6
Reflection
*PLUS
D resolution high: 3.4 Å / D resolution low: 3 Å / Number measured all: 297864
Reflection shell
*PLUS
Highest resolution: 3.4 Å / Percent possible obs: 80.6 / MeanI over sigI obs: 3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.0refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: H. influenzae HslU at 2.3A H. influenzae HslV at 1.9A

R Free selection details: RANDOM / Data cutoff high absF: 9712778.95 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 63.96 / Solvent model param ksol: 0.238
Displacement parametersB iso mean: 102.9 Å2 / Aniso B11: -28.95 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -7.75 Å2 / Aniso B23: 0 Å2 / Aniso B33: 36.7 Å2
Least-squares processR factor R free: 0.284 / R factor R free error: 0.004 / R factor R work: 0.24 / R factor obs: 0.24 / Highest resolution: 3.41 Å / Lowest resolution: 30.08 Å / Number reflection R free: 6383 / Number reflection all: 134912 / Number reflection obs: 126814 / Percent reflection R free: 5
Refine analyzeLuzzati coordinate error free: 0.49 Å / Luzzati coordinate error obs: 0.4 Å / Luzzati d res low obs: 5 Å
Refine hist #LASTHighest resolution: 3.41 Å / Lowest resolution: 30.08 Å
Number of atoms included #LASTProtein: 45156 / Nucleic acid: 0 / Ligand: 372 / Solvent: 0 / Total: 45528
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
Refine LS shellHighest resolution: 3.4 Å / R factor R free: 0.367 / R factor R free error: 0.013 / R factor R work: 0.344 / Lowest resolution: 3.61 Å / Number reflection R free: 852 / Number reflection R work: 15794 / Total number of bins used: 6 / Percent reflection R free: 5.1 / Percent reflection obs: 65.9
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BILL_DNA-RNA-ATP_REP.PARAMBILL_ATP.TOP2
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine
*PLUS
Sigma F: 0
Displacement parameters
*PLUS
B iso mean: 102.9 Å2
Least-squares process
*PLUS
R factor R work: 0.24 / R factor obs: 0.24 / Percent reflection R free: 5
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010
X-RAY DIFFRACTIONc_angle_deg1.30
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.80
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
Refine LS shell
*PLUS
Percent reflection R free: 5.1 / R factor R free: 0.367 / R factor R work: 0.344

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