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- PDB-3k1j: Crystal structure of Lon protease from Thermococcus onnurineus NA1 -

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Basic information

Entry
Database: PDB / ID: 3k1j
TitleCrystal structure of Lon protease from Thermococcus onnurineus NA1
ComponentsATP-dependent protease Lon
KeywordsHYDROLASE / ATP-dependent protease / ATP-binding / Nucleotide-binding / Protease
Function / homology
Function and homology information


ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / regulation of DNA-templated transcription / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
Lon protease, archaeal / LonB-like, AAA domain / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Lon proteolytic domain profile. ...Lon protease, archaeal / LonB-like, AAA domain / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Helicase, Ruva Protein; domain 3 - #60 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S5 domain 2-type fold, subgroup / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Archaeal Lon protease
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCha, S.S. / An, Y.J.
CitationJournal: Embo J. / Year: 2010
Title: Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber
Authors: Cha, S.S. / An, Y.J. / Lee, C.R. / Lee, H.S. / Kim, Y.G. / Kim, S.J. / Kwon, K.K. / De Donatis, G.M. / Lee, J.H. / Maurizi, M.R. / Kang, S.G.
History
DepositionSep 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent protease Lon
B: ATP-dependent protease Lon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1416
Polymers133,5622
Non-polymers1,5794
Water15,043835
1
A: ATP-dependent protease Lon
B: ATP-dependent protease Lon
hetero molecules

A: ATP-dependent protease Lon
B: ATP-dependent protease Lon
hetero molecules

A: ATP-dependent protease Lon
B: ATP-dependent protease Lon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)405,42418
Polymers400,6866
Non-polymers4,73812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area43510 Å2
ΔGint-68 kcal/mol
Surface area125910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.454, 121.454, 195.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-824-

HOH

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Components

#1: Protein ATP-dependent protease Lon / lon protease


Mass: 66780.984 Da / Num. of mol.: 2 / Mutation: S523A, K566A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YU74
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 295 K / Method: batch crystallization method / Details: batch crystallization method, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 109482 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.1 Å2
Reflection shellHighest resolution: 2 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.17 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 67288.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 5516 5 %RANDOM
Rwork0.206 ---
obs0.206 109482 99.7 %-
all-109812 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6378 Å2 / ksol: 0.334197 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å22.34 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8678 0 74 835 9587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 942 5.2 %
Rwork0.301 17169 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2ion.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3water_rep.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4adp.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5pg8.param&_1_TOPOLOGY_INFILE_6

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