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- PDB-8dvh: Crystal structure of ATP-dependent Lon protease from Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 8dvh
TitleCrystal structure of ATP-dependent Lon protease from Bacillus subtillis (BsLonBA)
ComponentsLon protease 2Lon protease family
KeywordsHYDROLASE / ATP-DEPENDENT PROTEASE / CATALYTIC SER-LYS DYAD
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm
Similarity search - Function
Sporulation protease LonB / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup ...Sporulation protease LonB / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-BO2 / Lon protease 2
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSekula, B. / Li, M. / Gustchina, A. / Wlodawer, A.
Funding support United States, Russian Federation, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
Russian Science FoundationRussian Science Foundation Russian Federation
CitationJournal: Int J Mol Sci / Year: 2022
Title: Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases.
Authors: Gustchina, A. / Li, M. / Andrianova, A.G. / Kudzhaev, A.M. / Lountos, G.T. / Sekula, B. / Cherry, S. / Tropea, J.E. / Smirnov, I.V. / Wlodawer, A. / Rotanova, T.V.
History
DepositionJul 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lon protease 2
B: Lon protease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3216
Polymers43,5062
Non-polymers8144
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.892, 89.892, 83.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Lon protease 2 / Lon protease family / ATP-dependent protease La 2


Mass: 21753.080 Da / Num. of mol.: 2 / Fragment: Proteolytic domain, residues 347-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: lon2, lonB, ysxF, BSU28210 / Plasmid: pDEST-527 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42425, endopeptidase La
#2: Chemical ChemComp-BO2 / N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / BORTEZOMIB / Bortezomib


Mass: 384.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25BN4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticancer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 35% PEG400 at pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→84 Å / Num. obs: 294057 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 39.59 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 30.1
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1942 / Rsym value: 0.827

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.27data extraction
REFMAC5.8.0258refinement
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rre

1rre


Resolution: 1.9→77.85 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.843 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 951 3.1 %RANDOM
Rwork0.1939 ---
obs0.1954 29451 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.22 Å2 / Biso mean: 43.785 Å2 / Biso min: 25.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0.68 Å2-0 Å2
2---1.36 Å20 Å2
3---4.41 Å2
Refinement stepCycle: final / Resolution: 1.9→77.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2831 0 58 159 3048
Biso mean--38.08 49.26 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132929
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172889
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.6543958
X-RAY DIFFRACTIONr_angle_other_deg1.3511.5926742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0955382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7225.922103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93315528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.808156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 73 -
Rwork0.316 2158 -
all-2231 -
obs--99.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3948-0.2313-0.03152.2616-0.57362.11180.0597-0.01190.0047-0.0386-0.04170.7621-0.22750.2364-0.0180.1535-0.0111-0.04770.23010.00630.299516.37722.846940.865
22.8816-1.1361.7940.4804-1.02214.4691-0.00340.0487-0.20750.0136-0.01720.0856-0.04880.0650.02070.25530.0004-0.04890.23430.00470.156430.949321.979844.5764
34.72120.59793.90490.09820.58674.47640.0229-0.11550.0336-0.0188-0.03180.04670.08880.07780.00880.24110.0093-0.02530.2388-0.01520.170433.939314.96545.4497
43.65910.5547-0.81721.38240.03350.7946-0.00310.48720.1437-0.2254-0.04710.27680.13880.08170.05030.32650.0516-0.09480.3161-0.00090.078723.738816.792528.1532
51.5496-0.3043-0.380.8946-0.35550.35070.01670.0505-0.1648-0.01110.080.378-0.00640.019-0.09670.184-0.0305-0.04890.22280.02280.278814.450614.596143.9269
64.1371-0.5573-0.62681.0935-1.66133.32010.11160.3827-0.6218-0.3670.23160.52940.6721-0.417-0.34320.1557-0.085-0.08440.13080.0760.61247.61767.729744.5064
70.49970.0920.56782.5722-1.62584.18760.0946-0.0623-0.22140.12880.04270.324-0.1068-0.0644-0.13730.24990.0019-0.01460.23090.00870.21433.6225-2.338847.1309
83.59432.22692.94051.54341.44473.3468-0.17170.1675-0.1743-0.08710.1774-0.1458-0.29980.0658-0.00570.2911-0.013-0.02160.2411-0.04770.118643.566813.527342.5391
91.11760.3492-0.18571.66250.76780.4837-0.10560.199-0.0924-0.09950.1523-0.1494-0.0729-0.0076-0.04680.2732-0.01840.01590.2584-0.06110.134541.65154.605536.7799
101.29781.6158-0.28092.4991-0.83310.5618-0.10840.1504-0.4498-0.0890.2462-0.35330.0535-0.1142-0.13780.2328-0.0032-0.03670.1462-0.06080.288541.0812-10.455344.2185
111.67691.1993.36720.98292.58697.02080.17310.05390.02230.09010.021-0.1620.27460.061-0.19420.3602-0.10860.06720.2309-0.06690.300335.6965-13.475226.8266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B348 - 382
2X-RAY DIFFRACTION2B383 - 396
3X-RAY DIFFRACTION3B397 - 418
4X-RAY DIFFRACTION4B419 - 433
5X-RAY DIFFRACTION5B434 - 506
6X-RAY DIFFRACTION6B507 - 535
7X-RAY DIFFRACTION7A352 - 373
8X-RAY DIFFRACTION8A374 - 406
9X-RAY DIFFRACTION9A407 - 446
10X-RAY DIFFRACTION10A447 - 524
11X-RAY DIFFRACTION11A525 - 547

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