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- PDB-5ji2: HslU L199Q in HslUV complex -

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Basic information

Entry
Database: PDB / ID: 5ji2
TitleHslU L199Q in HslUV complex
Components
  • ATP-dependent protease ATPase subunit HslU
  • ATP-dependent protease subunit HslV
KeywordsHYDROLASE / AAA+ ATPase / peptidase
Function / homology
Function and homology information


HslU-HslV peptidase / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / 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 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / 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 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Helicase, Ruva Protein; domain 3 / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 4-Layer Sandwich / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease subunit HslV / ATP-dependent protease ATPase subunit HslU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.307 Å
AuthorsGrant, R.A. / Sauer, R.T. / Schmitz, K.R. / Baytshtok, V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI016892-36 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM1011988-37 United States
Citation
Journal: Structure / Year: 2016
Title: A Structurally Dynamic Region of the HslU Intermediate Domain Controls Protein Degradation and ATP Hydrolysis.
Authors: Baytshtok, V. / Fei, X. / Grant, R.A. / Baker, T.A. / Sauer, R.T.
#1: Journal: Structure / Year: 2001
Title: Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism.
Authors: Wang, J. / Song, J.J. / Franklin, M.C. / Kamtekar, S. / Im, Y.J. / Rho, S.H. / Seong, I.S. / Lee, C.S. / Chung, C.H. / Eom, S.H.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence / Database references
Category: citation / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,82611
Polymers181,8996
Non-polymers9275
Water0
1
A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4954
Polymers40,4462
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4703
Polymers40,4462
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8624
Polymers101,0072
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.005, 170.005, 163.385
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

#1: Protein
ATP-dependent protease subunit HslV / Heat shock protein HslV


Mass: 20223.006 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain 55989 / EAEC) (bacteria)
Strain: 55989 / EAEC / Gene: hslV, EC55989_4410 / Production host: Escherichia coli (E. coli) / References: UniProt: B7LA29, HslU-HslV peptidase
#2: Protein ATP-dependent protease ATPase subunit HslU / Heat shock protein HslU / Unfoldase HslU


Mass: 50503.551 Da / Num. of mol.: 2 / Mutation: L199Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: hslU, htpI, Z5478, ECs4858 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6H6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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: 3.75 Å3/Da / Density % sol: 67.17 % / Description: hexagonal plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 1.8 M Ammonium Sulfate, 7.5 mg/ml HslU(L199Q), 9.7 mg/ml HslV, 5 mM ATP, 0.5 mg/ml Arc-st11-ssrA (synthetic peptide substrate)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 3.3→50 Å / Num. obs: 41171 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.045 / Rrim(I) all: 0.149 / Χ2: 1.149 / Net I/av σ(I): 20.976 / Net I/σ(I): 6.2 / Num. measured all: 450056
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.3-3.369.81.5091100
3.36-3.4210.61.281100
3.42-3.48111.0891100
3.48-3.5511.10.8481100
3.55-3.6311.10.6971100
3.63-3.7211.10.4931100
3.72-3.8111.20.5191100
3.81-3.9111.20.3721100
3.91-4.0311.30.3281100
4.03-4.1611.20.2481100
4.16-4.3111.20.1971100
4.31-4.4811.20.1531100
4.48-4.6811.20.1251100
4.68-4.9311.20.1151100
4.93-5.2411.10.1161100
5.24-5.64110.1171100
5.64-6.21110.1181100
6.21-7.110.80.0951100
7.1-8.9410.50.0521100
8.94-50100.0381100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G4A

1g4a


Resolution: 3.307→49.076 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8
RfactorNum. reflection% reflection
Rfree0.2811 2003 4.87 %
Rwork0.2356 --
obs0.2385 41171 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 202.4 Å2 / Biso mean: 125.4572 Å2 / Biso min: 48.3 Å2
Refinement stepCycle: final / Resolution: 3.307→49.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10975 0 81 0 11056
Biso mean--94.48 --
Num. residues----1424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311165
X-RAY DIFFRACTIONf_angle_d0.54215086
X-RAY DIFFRACTIONf_chiral_restr0.0541777
X-RAY DIFFRACTIONf_plane_restr0.0031950
X-RAY DIFFRACTIONf_dihedral_angle_d19.514172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.309-3.39170.3671420.316827592901
3.3917-3.48340.32461390.315427492888
3.4834-3.58590.29381430.315927622905
3.5859-3.70150.33911440.320827812925
3.7015-3.83370.33891350.286627532888
3.8337-3.98710.32951430.266327782921
3.9871-4.16840.27061440.254927632907
4.1684-4.3880.28761430.240127782921
4.388-4.66260.28011430.211727762919
4.6626-5.02210.28251440.209328002944
5.0221-5.52650.27761420.219827912933
5.5265-6.3240.30321420.241628252967
6.324-7.9590.2281470.208828422989
7.959-42.50470.24491520.229653117

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