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- PDB-4git: Crystal structure of alpha sub-domain of Lon protease from Brevib... -

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Basic information

Entry
Database: PDB / ID: 4git
TitleCrystal structure of alpha sub-domain of Lon protease from Brevibacillus thermoruber
ComponentsLon protease
KeywordsHYDROLASE / DNA binding
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 binding / cytoplasm
Similarity search - Function
Lon protease, bacterial / 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 N-terminal domain profile. / Lon protease, N-terminal domain ...Lon protease, bacterial / 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 N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Helicase, Ruva Protein; domain 3 - #60 / PUA-like superfamily / Helicase, Ruva Protein; domain 3 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBrevibacillus thermoruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.882 Å
AuthorsChen, Y.D. / Chang, Y.Y. / Hsu, C.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis for DNA-mediated allosteric regulation facilitated by the AAA(+) module of Lon protease.
Authors: Lee, A.Y. / Chen, Y.D. / Chang, Y.Y. / Lin, Y.C. / Chang, C.F. / Huang, S.J. / Wu, S.H. / Hsu, C.H.
History
DepositionAug 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: 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 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,8934
Polymers28,7012
Non-polymers1922
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-22 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.283, 94.283, 94.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Lon protease


Mass: 14350.596 Da / Num. of mol.: 2 / Fragment: alpha sub-domain, UNP RESIDUES 491-605
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus thermoruber (bacteria) / Strain: WR-249 / Gene: lon / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84FG5, endopeptidase La
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1M potassium phosphate, 0.2M sodium chloride, 12.5% PEG 8000, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 19, 2010
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.88→30 Å / Num. all: 6542 / Num. obs: 6542 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.88 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 38 / Num. unique all: 6523 / Rsym value: 0.504

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M6A

3m6a


Resolution: 2.882→29.815 Å / SU ML: 0.4 / σ(F): 1.38 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 643 9.84 %RANDOM
Rwork0.2013 ---
obs0.2061 6534 99.69 %-
all-6542 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.236 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.882→29.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 10 4 1506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091516
X-RAY DIFFRACTIONf_angle_d1.3172026
X-RAY DIFFRACTIONf_dihedral_angle_d16.262618
X-RAY DIFFRACTIONf_chiral_restr0.093224
X-RAY DIFFRACTIONf_plane_restr0.006258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8823-3.10460.3521320.29531161100
3.1046-3.41670.32391280.23521153100
3.4167-3.91010.28711290.20511170100
3.9101-4.92280.1951260.16971181100
4.9228-29.81650.22881280.1949122699
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)
17.6171.3485-1.42934.99453.06264.4360.26570.5872-0.03960.3977-0.2523-1.4304-1.33720.0214-0.93530.4441-0.1884-0.05090.64340.38180.642819.74-8.354141.793
26.86491.0239-4.05789.0528-3.47799.2070.31760.88360.35960.44250.0506-0.1056-0.2748-0.4871-0.16860.4555-0.06650.0830.60010.2180.270121.594-6.683131.589
36.27731.5715-3.79442.858-3.54975.03560.79010.66841.76830.77450.20391.1067-0.8139-1.3149-0.93250.8960.20240.11921.39850.22530.628521.684-10.769121.095
43.67670.0435-1.78527.3497-4.20164.18790.0866-0.4689-0.76371.3297-0.4307-0.3863-0.307-0.2969-0.47620.5692-0.4318-0.00890.69070.15760.38347.4678.367114.034
57.33613.2115-5.98546.4492-1.13836.16640.07930.7407-0.26890.5147-0.208-0.05250.2054-1.1351-0.12650.4549-0.18090.05470.64740.13850.427436.9646.941114.222
68.72360.72590.51186.4557-0.56155.9844-0.19060.5612-0.3273-0.8089-0.3642-1.27781.25430.02990.4820.4775-0.27360.25790.75850.03180.607139.1625.351123.023
74.313-0.5072-0.5240.65731.14262.02620.05952.8145-0.1575-0.4878-0.11280.40660.8794-0.95630.89420.7662-0.49390.18641.529-0.20770.760625.6029.591114.469
82.2552.37373.24623.61230.929120.53130.4821-3.33280.8865-0.2375-2.9022.5348-0.2188-0.52161.00380.3594-0.15971.1113-0.06511.851433.35817.718124.252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 492:503)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 504:548)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 549:582)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 492:503)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 504:540)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 541:548)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 549:577)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 578:582)

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