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- PDB-3m65: Crystal structure of Bacillus subtilis Lon N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3m65
TitleCrystal structure of Bacillus subtilis Lon N-terminal domain
ComponentsATP-dependent protease La 1Endopeptidase La
KeywordsHYDROLASE / coiled-coil / ATP-binding / nucleotide-binding / protease / serine protease / stress response
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Lon protease, bacterial / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Lon protease, bacterial / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Lon protease, bacterial/eukaryotic-type / 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 / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDuman, R.E. / Lowe, J.Y.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of Bacillus subtilis Lon Protease.
Authors: Duman, R.E. / Lowe, J.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 La 1
B: ATP-dependent protease La 1


Theoretical massNumber of molelcules
Total (without water)48,0272
Polymers48,0272
Non-polymers00
Water64936
1
A: ATP-dependent protease La 1


Theoretical massNumber of molelcules
Total (without water)24,0141
Polymers24,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent protease La 1


Theoretical massNumber of molelcules
Total (without water)24,0141
Polymers24,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-60 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.877, 81.759, 115.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 9:53 )
211chain B and (resseq 9:53 )
112chain A and (resseq 57:115 )
212chain B and (resseq 57:115 )
113chain A and (resseq 123:208 )
213chain B and (resseq 123:208 )

NCS ensembles :
ID
1
2
3

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Components

#1: Protein ATP-dependent protease La 1 / Endopeptidase La


Mass: 24013.564 Da / Num. of mol.: 2 / Fragment: BsLon, N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU28200, lon, lonA / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: P37945, endopeptidase La
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M Sodium Citrate, 5% PEG 6000, pH 4, vapor diffusion, sitting drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→41 Å / Num. all: 13996 / Num. obs: 13088 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.085 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1899 / Rsym value: 0.362 / % possible all: 99.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_129)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ANE

2ane


Resolution: 2.6→41 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / σ(F): 1.09 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1167 4.93 %random
Rwork0.1914 ---
obs0.1954 23671 96.2 %-
all-24606 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.11 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.1859 Å20 Å2-0 Å2
2--6.7462 Å2-0 Å2
3----2.5603 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 0 36 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083336
X-RAY DIFFRACTIONf_angle_d1.0814500
X-RAY DIFFRACTIONf_dihedral_angle_d18.8691284
X-RAY DIFFRACTIONf_chiral_restr0.078532
X-RAY DIFFRACTIONf_plane_restr0.004574
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A356X-RAY DIFFRACTIONPOSITIONAL0.041
12B356X-RAY DIFFRACTIONPOSITIONAL0.041
21A475X-RAY DIFFRACTIONPOSITIONAL0.038
22B475X-RAY DIFFRACTIONPOSITIONAL0.038
31A693X-RAY DIFFRACTIONPOSITIONAL0.04
32B693X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71830.35821140.25372902X-RAY DIFFRACTION98
2.7183-2.86160.33021550.24052814X-RAY DIFFRACTION97
2.8616-3.04080.3251430.22172815X-RAY DIFFRACTION97
3.0408-3.27550.30521740.20742822X-RAY DIFFRACTION97
3.2755-3.6050.29541580.17422827X-RAY DIFFRACTION97
3.605-4.12620.23151150.16252833X-RAY DIFFRACTION96
4.1262-5.1970.20171380.1292797X-RAY DIFFRACTION96
5.197-410.21711700.17642694X-RAY DIFFRACTION93
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)
10.22630.04210.13270.38130.07870.192-0.0312-0.003-00.110.02870.0132-0.07020.0253-0.01520.1858-0.0076-0.00110.18720.02010.1042-59.626-8.847619.474
21.1220.5960.19970.30890.13180.13150.2148-0.1731-0.048-0.0773-0.14510.07640.1070.0009-0.04680.09360.0112-0.0058-0.01790.01340.0916-40.1593-16.966145.3267
30.95190.28330.37080.2497-0.18360.6077-0.00650.0436-0.0010.22830.32280.13730.14210.19420.36860.13540.042-0.0230.17720.00870.1474-23.88891.783249.2433
41.0718-0.24640.58330.1428-0.02350.36940.2534-0.14070.02160.1993-0.213-0.04550.1159-0.00390.1830.1408-0.04550.00020.1041-0.06960.1986-42.1397-21.50933.4539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 3:116A3 - 116
2X-RAY DIFFRACTION2chain A and resseq 123:208A123 - 208
3X-RAY DIFFRACTION3chain B and resseq 3:124B3 - 124
4X-RAY DIFFRACTION4chain B and resseq 125:208B125 - 208

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