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- PDB-4zpx: Crystal structure of Lon ATPase domain from Thermococcus onnurine... -

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Basic information

Entry
Database: PDB / ID: 4zpx
TitleCrystal structure of Lon ATPase domain from Thermococcus onnurineus NA1
ComponentsATP-dependent protease Lon
KeywordsHYDROLASE / AAA+ proteins / PS-1 insert / H2 insert / Ins1 / Lon Protease / Thermococcus onnurineus NA1 / ATP-independent proteolytic activity
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 / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / 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, archaeal / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / 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 / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Archaeal Lon protease
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsAn, Y.J. / Kim, M.I. / Na, J.H. / Cha, S.S.
CitationJournal: To Be Published
Title: Structural disparity classifies AAA+ modules of Lon proteases into two distinct clades
Authors: Kim, M.I. / An, Y.J. / Na, J.H. / Cha, S.S.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 Lon
B: ATP-dependent protease Lon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0513
Polymers91,9592
Non-polymers921
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-0 kcal/mol
Surface area29490 Å2
Unit cell
Length a, b, c (Å)40.620, 61.599, 76.321
Angle α, β, γ (deg.)74.61, 87.11, 83.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ATP-dependent protease Lon


Mass: 45979.539 Da / Num. of mol.: 2 / Fragment: UNP residues 1-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0529 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YU74
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.2M Potassium chloride, 0.01M Magnesium acetate, 0.05M tri-sodium citrate dihydrate pH 4.5, 12% PEG 4000, 5% n-Dodecyl-beta-D-maltoside

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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: Feb 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 42270 / % possible obs: 93.1 % / Redundancy: 2.3 % / Net I/σ(I): 23.03

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→41.14 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.799 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 2130 5 %RANDOM
Rwork0.18157 ---
obs0.18444 40140 92.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.085 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å21.91 Å2-0.52 Å2
2---0.52 Å2-0.44 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.03→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4960 0 6 243 5209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195038
X-RAY DIFFRACTIONr_bond_other_d0.0010.025076
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.986815
X-RAY DIFFRACTIONr_angle_other_deg0.9233.00111647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89823.695203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91715882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1091542
X-RAY DIFFRACTIONr_chiral_restr0.1190.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215649
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021049
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8973.1592625
X-RAY DIFFRACTIONr_mcbond_other2.8973.1572624
X-RAY DIFFRACTIONr_mcangle_it4.2534.7073269
X-RAY DIFFRACTIONr_mcangle_other4.2534.7093270
X-RAY DIFFRACTIONr_scbond_it3.7663.5822413
X-RAY DIFFRACTIONr_scbond_other3.7643.5822413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7495.2013547
X-RAY DIFFRACTIONr_long_range_B_refined8.13429.59921269
X-RAY DIFFRACTIONr_long_range_B_other8.12329.58221178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.035→2.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 133 -
Rwork0.227 2515 -
obs--79.81 %

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