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- PDB-1im2: HslU, Haemophilus Influenzae, Selenomethionine Variant -

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Basic information

Entry
Database: PDB / ID: 1im2
TitleHslU, Haemophilus Influenzae, Selenomethionine Variant
ComponentsATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
KeywordsCHAPERONE / AAA family
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: 2.8 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: 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.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Mutational Studies on HslU and its Docking Mode with HslV
Authors: Song, H.K. / Hartmann, C. / Ramachandran, R. / Bochtler, M. / Behrendt, R. / Moroder, L. / Huber, R.
#3: 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.
History
DepositionMay 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6683
Polymers50,1451
Non-polymers5232
Water00
1
A: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)304,00918
Polymers300,8706
Non-polymers3,14012
Water0
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)109.826, 109.826, 313.675
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
DetailsThere are 2 molecules in the asymetric unit, because of twinning we observe only one (ref entry 1G41). The biological structure consists of hexamer which packs into dodecamer with 622 symmetry.

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Components

#1: Protein ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU / HEAT SHOCK PROTEIN HSLU


Mass: 50144.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: PRSET / Production host: Escherichia coli (E. coli) / Strain (production host): B834(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
Has protein modificationY

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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: 5.45 Å3/Da
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 2000 MME, lithium sulphate, magnesium sulphate, zink sulphate, tricine, europium chloride, ADP, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 M1dropKCl
25 mMbeta-mercaptoethanol1drop
31 mM1dropMgCl2
420 mMpotassium phosphate1drop
510 mMADP1drop
610 %PEG2000 MME1reservoir
70.6 M1reservoirLiSO4
86 %ethanol1reservoir
910 mM1reservoirMgSO4
101 mM1reservoirZnSO4
113 mM1reservoirEuCl3
12100 mMtricine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.925, 0.979, 1.068
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 1999 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9251
20.9791
31.0681
ReflectionResolution: 2.8→40 Å / Num. all: 47257 / Num. obs: 43125 / % possible obs: 90.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1350 / Rsym value: 0.305 / % possible all: 61.3
Reflection
*PLUS
Num. measured all: 190830
Reflection shell
*PLUS
% possible obs: 61.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G41

1g41


Resolution: 2.8→37.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 235868.52 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / 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
Rfree0.25 4235 9.8 %RANDOM
Rwork0.233 ---
all0.2342 52218 --
obs0.233 43125 82.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.6 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 57.6 Å2
Baniso -1Baniso -2Baniso -3
1--24.69 Å2-2.66 Å20 Å2
2---24.69 Å20 Å2
3---49.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.8→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 32 0 2729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 417 9.9 %
Rwork0.425 3785 -
obs--48.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3MOD19-CIS_PEPTIDE.PARAMADP_XPLOR.TOP
X-RAY DIFFRACTION4ADP_XPLOR_PAR.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 57.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.419 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.425

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