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- PDB-1yyf: Correction of X-ray Intensities from an HslV-HslU co-crystal cont... -

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Basic information

Entry
Database: PDB / ID: 1yyf
TitleCorrection of X-ray Intensities from an HslV-HslU co-crystal containing lattice translocation defects
Components
  • ATP-dependent hsl protease ATP-binding subunit hslU
  • ATP-dependent protease hslV
KeywordsCHAPERONE/HYDROLASE / Lattice translocation Defect / HslV-HslU / ATP-dependent proteolysis / Quaternary Structure / CHAPERONE-HYDROLASE COMPLEX
Function / homology
Function and homology information


protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / protein unfolding / threonine-type endopeptidase activity / serine-type peptidase activity / proteolysis involved in protein catabolic process / peptidase activity ...protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / protein unfolding / threonine-type endopeptidase activity / serine-type peptidase activity / 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 / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease ATPase subunit HslU / ATP-dependent protease subunit ClpQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.16 Å
AuthorsWang, J. / Rho, S.H. / Park, H.H. / Eom, S.H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Correction of X-ray intensities from an HslV-HslU co-crystal containing lattice-translocation defects.
Authors: Wang, J. / Rho, S.H. / Park, H.H. / Eom, S.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Correction of X-ray intensities from single crystals with lattice translocation defects
Authors: Wang, J. / Kamtekar, S. / Berman, A.J. / Steitz, T.A.
#2: Journal: J.Struct.Biol. / Year: 2003
Title: A second response in correcting the HslV-HslU quaternary structure
Authors: Wang, J.
#3: Journal: J.Struct.Biol. / Year: 2001
Title: The quaternary arrangement of HslU and HslV in a co-crystal: A response to Wang, Yale
Authors: Bochtler, M. / Song, H.K. / Hartmann, C. / Ramachandran, R. / Huber, R.
#4: Journal: J.Struct.Biol. / Year: 2001
Title: A corrected quaternary arrangement of the peptidase HslV and ATPase HslU in a cocrystal structure
Authors: Wang, J.
#5: 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
DepositionFeb 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: ATP-dependent hsl protease ATP-binding subunit hslU
B: ATP-dependent hsl protease ATP-binding subunit hslU
D: ATP-dependent protease hslV
C: ATP-dependent protease hslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1806
Polymers138,3264
Non-polymers8542
Water00
1
A: ATP-dependent hsl protease ATP-binding subunit hslU
B: ATP-dependent hsl protease ATP-binding subunit hslU
D: ATP-dependent protease hslV
C: ATP-dependent protease hslV
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)835,08336
Polymers829,95624
Non-polymers5,12612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Unit cell
Length a, b, c (Å)181.196, 181.196, 529.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12A
22B
13A
23B
14C
24D
34C
44D
15C
25D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETVALVAL1AA1 - 961 - 96
211METMETVALVAL1BB1 - 961 - 96
321HISHISALAALA2AA250 - 334250 - 334
421HISHISALAALA2BB250 - 334250 - 334
112ASPASPGLNGLN1AA97 - 24997 - 249
212ASPASPGLNGLN1BB97 - 24997 - 249
113LEULEULEULEU1AA335 - 443335 - 443
213LEULEULEULEU1BB335 - 443335 - 443
114SERSERGLNGLN1CD2 - 302 - 30
214SERSERGLNGLN1DC2 - 302 - 30
324GLYGLYGLUGLU2CD125 - 181125 - 181
424GLYGLYGLUGLU2DC125 - 181125 - 181
115ALAALAASPASP1CD31 - 12431 - 124
215ALAALAASPASP1DC31 - 12431 - 124

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein ATP-dependent hsl protease ATP-binding subunit hslU / Heat shock protein hslU


Mass: 49659.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hslU, htpI / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6H5
#2: Protein ATP-dependent protease hslV


Mass: 19503.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hslV, clpQ, codW / Production host: Escherichia coli (E. coli)
References: UniProt: P39070, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, 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: 6.05 Å3/Da / Density % sol: 79.67 %
Crystal growMethod: evaporation / Details: EVAPORATION

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B
DetectorDetector: IMAGE PLATE / Date: Mar 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.16→34.92 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.751 / SU B: 55.109 / SU ML: 0.725 / Cross valid method: THROUGHOUT / ESU R Free: 0.894 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.34572 1299 5.1 %RANDOM
Rwork0.27668 ---
all0.28 ---
obs0.2802 24225 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.45 Å2
Baniso -1Baniso -2Baniso -3
1-8.23 Å24.11 Å20 Å2
2--8.23 Å20 Å2
3----12.34 Å2
Refinement stepCycle: LAST / Resolution: 4.16→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9161 0 54 0 9215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0219164
X-RAY DIFFRACTIONr_angle_refined_deg2.9041.97112394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.11651170
X-RAY DIFFRACTIONr_chiral_restr0.1750.21448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026812
X-RAY DIFFRACTIONr_nbd_refined0.3730.25581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2870.2580
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3740.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3310.214
X-RAY DIFFRACTIONr_mcbond_it0.9851.55830
X-RAY DIFFRACTIONr_mcangle_it1.92929338
X-RAY DIFFRACTIONr_scbond_it2.30433334
X-RAY DIFFRACTIONr_scangle_it4.3184.53056
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1095tight positional0.090.05
2A906tight positional0.090.05
3A845tight positional0.110.05
4C440tight positional0.070.05
5C734tight positional0.070.05
1A301medium positional0.290.5
4C175medium positional0.220.5
1A1095tight thermal0.110.5
2A906tight thermal0.10.5
3A845tight thermal0.110.5
4C440tight thermal0.090.5
5C734tight thermal0.10.5
1A301medium thermal0.792
4C175medium thermal0.722
LS refinement shellResolution: 4.16→4.377 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.375 176
Rwork0.303 3412

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