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- PDB-6kr1: ATP dependent protease HslV from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 6kr1
TitleATP dependent protease HslV from Staphylococcus aureus
ComponentsATP-dependent protease subunit HslV
KeywordsHYDROLASE / Threonine prtease / HslUV / bacterial proteasome
Function / homology
Function and homology information


HslU-HslV peptidase / HslUV protease complex / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / metal ion binding
Similarity search - Function
ATP-dependent protease, HslV subunit / 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 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHa, N.-C. / Jeong, S.
CitationJournal: Mol.Cells / Year: 2020
Title: Cleavage-Dependent Activation of ATP-Dependent Protease HslUV from Staphylococcus aureus .
Authors: Jeong, S. / Ahn, J. / Kwon, A.R. / Ha, N.-C.
History
DepositionAug 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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
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 subunit HslV
F: ATP-dependent protease subunit HslV
G: ATP-dependent protease subunit HslV
H: ATP-dependent protease subunit HslV
I: ATP-dependent protease subunit HslV
J: ATP-dependent protease subunit HslV
K: ATP-dependent protease subunit HslV
L: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,30721
Polymers248,44312
Non-polymers8659
Water17,853991
1
A: ATP-dependent protease subunit HslV
F: ATP-dependent protease subunit HslV
L: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3035
Polymers62,1113
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-41 kcal/mol
Surface area22240 Å2
MethodPISA
2
B: ATP-dependent protease subunit HslV
G: ATP-dependent protease subunit HslV
H: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3996
Polymers62,1113
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-59 kcal/mol
Surface area21830 Å2
MethodPISA
3
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
I: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3035
Polymers62,1113
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-38 kcal/mol
Surface area21720 Å2
MethodPISA
4
E: ATP-dependent protease subunit HslV
J: ATP-dependent protease subunit HslV
K: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3035
Polymers62,1113
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-37 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.304, 94.304, 227.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein
ATP-dependent protease subunit HslV


Mass: 20703.564 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Gene: hslV, clpQ, SAV1253 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P65796, HslU-HslV peptidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES:NaOH, Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 150435 / % possible obs: 98.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.48 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.082 / Net I/σ(I): 17.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7367 / Rpim(I) all: 0.26 / Rrim(I) all: 0.526 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YYF

1yyf


Resolution: 2→33.16 Å / SU ML: 0.3074 / Cross valid method: FREE R-VALUE / σ(F): 2.18 / Phase error: 27.4435
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2659 6166 4.9 %
Rwork0.2163 119619 -
obs0.2187 125785 82.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.85 Å2
Refinement stepCycle: LAST / Resolution: 2→33.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15548 0 45 991 16584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001415754
X-RAY DIFFRACTIONf_angle_d0.377721212
X-RAY DIFFRACTIONf_chiral_restr0.04192467
X-RAY DIFFRACTIONf_plane_restr0.00112731
X-RAY DIFFRACTIONf_dihedral_angle_d2.07199478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.4468180.2591435X-RAY DIFFRACTION8.99
2.02-2.050.3706370.3007616X-RAY DIFFRACTION12.78
2.05-2.070.3469430.302925X-RAY DIFFRACTION19.22
2.07-2.10.289390.30111399X-RAY DIFFRACTION27.7
2.1-2.120.349890.29772012X-RAY DIFFRACTION42.24
2.12-2.150.38371290.29382697X-RAY DIFFRACTION55
2.15-2.180.33952270.28273332X-RAY DIFFRACTION70.38
2.18-2.220.31721670.27513921X-RAY DIFFRACTION79.98
2.22-2.250.34742470.28034164X-RAY DIFFRACTION86.49
2.25-2.290.37042260.26844402X-RAY DIFFRACTION91.3
2.29-2.330.32122430.26234612X-RAY DIFFRACTION94.88
2.33-2.370.34362390.27094699X-RAY DIFFRACTION96.54
2.37-2.420.28511630.26754823X-RAY DIFFRACTION97.25
2.42-2.470.29872550.24634694X-RAY DIFFRACTION97.79
2.47-2.520.33532950.25154714X-RAY DIFFRACTION98.68
2.52-2.580.27671930.24664832X-RAY DIFFRACTION98.92
2.58-2.640.25032570.25334811X-RAY DIFFRACTION99.28
2.64-2.710.27552120.24664883X-RAY DIFFRACTION99.41
2.71-2.790.34392280.2534842X-RAY DIFFRACTION99.37
2.79-2.880.28853090.24334736X-RAY DIFFRACTION99.31
2.88-2.990.29132540.23174805X-RAY DIFFRACTION99.68
2.99-3.110.27292770.23114821X-RAY DIFFRACTION99.84
3.11-3.250.25422680.22784895X-RAY DIFFRACTION99.85
3.25-3.420.28732260.20034794X-RAY DIFFRACTION99.92
3.42-3.630.28352110.18814921X-RAY DIFFRACTION99.88
3.63-3.910.23442720.16974809X-RAY DIFFRACTION99.92
3.91-4.30.22352430.16924867X-RAY DIFFRACTION99.84
4.3-4.930.18372960.15664766X-RAY DIFFRACTION99.9
4.93-6.20.252480.18034834X-RAY DIFFRACTION99.96
6.2-33.160.19582550.19074558X-RAY DIFFRACTION94.28

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