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- PDB-1g41: CRYSTAL STRUCTURE OF HSLU HAEMOPHILUS INFLUENZAE -

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Basic information

Entry
Database: PDB / ID: 1g41
TitleCRYSTAL STRUCTURE OF HSLU HAEMOPHILUS INFLUENZAE
ComponentsHEAT SHOCK PROTEIN HSLU
KeywordsCHAPERONE / AAA-ATPASE / CLPY / ATP-DEPENDENT PROTEOLYSIS
Function / homology
Function and homology information


HslUV protease complex / proteasome-activating activity / protein unfolding / proteolysis involved in protein catabolic process / peptidase activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
Heat shock protein HslU / : / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / 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 / ATPase family associated with various cellular activities (AAA) ...Heat shock protein HslU / : / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / 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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease ATPase subunit HslU
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTrame, C.B. / McKay, D.B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Haemophilus influenzae HslU protein in crystals with one-dimensional disorder twinning.
Authors: Trame, C.B. / McKay, D.B.
#1: Journal: 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.
#2: Journal: Nature / Year: 2000
Title: The Structures of HslU and the ATP-dependent Protease HslU-HslV
Authors: Bochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R.
History
DepositionOct 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9653
Polymers49,4421
Non-polymers5232
Water1,72996
1
A: HEAT SHOCK PROTEIN HSLU
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)299,78918
Polymers296,6496
Non-polymers3,14012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Unit cell
Length a, b, c (Å)110.620, 110.620, 335.83
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

DetailsThe biological assembly is a hexamer generated from a protomer in the asymmetric unit by the operations: -Y,X-Y,Z and Y-X,-X,Z and -X,-Y,Z and Y,Y-X,Z and X-Y,X,Z

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Components

#1: Protein HEAT SHOCK PROTEIN HSLU


Mass: 49441.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HSLU / Plasmid: PRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43773
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.3
Details: PEGMME 2000, lithium sulphate, MPD, magnesium sulphate, ADP, pH 7.3, VAPOR DIFFUSION, temperature 291.0K
Crystal grow
*PLUS
Temperature: 291 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-20 mg/mlprotein1drop
20.1 M1dropKCl
35 mMbeta-mercaptoethanol1drop
41 mM1dropMgCl2
520 mMpotassium phosphate1drop
67 mMADP1drop
710 %PEG2000MME1reservoir
80.38 M1reservoirLiSO4
94 mM1reservoirMgSO4
106 %MPD1reservoir
11100 mMtricine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2000 / Details: double crystal monochromator, mirrors
RadiationMonochromator: Double-Crystal Si 111 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→35.4 Å / Num. all: 53223 / Num. obs: 53223 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.17 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 5.8 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 8.5 / Num. unique all: 2563 / Rsym value: 12.4 / % possible all: 95.3
Reflection
*PLUS
Num. measured all: 168887
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 95.3 %

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DO0

1do0


Resolution: 2.3→35.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 250583.9 / Isotropic thermal model: group / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Twinning in the crystal produces the P 622 space group and an extended unit cell. Refinement was performed in this setting for one molecule in the asymmetric unit. Please see journal ...Details: Twinning in the crystal produces the P 622 space group and an extended unit cell. Refinement was performed in this setting for one molecule in the asymmetric unit. Please see journal citation for additional details.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 4983 10.1 %RANDOM
Rwork0.264 ---
all0.264 53223 --
obs0.264 49568 89.9 %-
Solvent computationSolvent model: flat model / Bsol: 36.3531 Å2 / ksol: 0.33177 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1--22.42 Å2-0.56 Å20 Å2
2---22.42 Å20 Å2
3---44.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 32 97 2696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
X-RAY DIFFRACTIONx_improper_angle_d1.14
X-RAY DIFFRACTIONx_mcbond_it7.1
X-RAY DIFFRACTIONx_mcangle_it11
X-RAY DIFFRACTIONx_scbond_it11.1
X-RAY DIFFRACTIONx_scangle_it15.8
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 743 10 %
Rwork0.387 --
obs-6707 83.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.paramwater.top
X-RAY DIFFRACTION3ion.paramwater_protin.top
X-RAY DIFFRACTION4adp_xplor_par.paramion.top
X-RAY DIFFRACTION5water_rep.param
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 35.4 Å / σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it11.1
X-RAY DIFFRACTIONc_mcangle_it11
X-RAY DIFFRACTIONc_scangle_it15.8
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.394 / % reflection Rfree: 10 % / Rfactor Rwork: 0.387 / Rfactor obs: 0.387

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