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- PDB-4ypl: Crystal structure of a hexameric LonA protease bound to three ADPs -

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Basic information

Entry
Database: PDB / ID: 4ypl
TitleCrystal structure of a hexameric LonA protease bound to three ADPs
ComponentsLon proteaseLon protease family
KeywordsHYDROLASE / Lon protease / ADP / MMH8709 / Inhibitor / AAA+ domain
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 / identical protein 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 protease, N-terminal domain superfamily / Lon N-terminal domain profile. ...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 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 / 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-4KZ / ADENOSINE-5'-DIPHOSPHATE / Lon protease
Similarity search - Component
Biological speciesMeiothermus taiwanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsLin, C.-C. / Chang, C.-I.
CitationJournal: Structure / Year: 2016
Title: Structural Insights into the Allosteric Operation of the Lon AAA+ Protease
Authors: Lin, C.-C. / Su, S.-C. / Su, M.-Y. / Liang, P.-H. / Feng, C.-C. / Wu, S.-H. / Chang, C.-I.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Feb 5, 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 1.4Nov 8, 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: Lon protease
B: Lon protease
C: Lon protease
F: Lon protease
D: Lon protease
E: Lon protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,76715
Polymers367,9766
Non-polymers3,7919
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24870 Å2
ΔGint-52 kcal/mol
Surface area136640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.044, 169.128, 135.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 61329.273 Da / Num. of mol.: 6
Fragment: AAA+ domain, protease domain, UNP residues 242-793
Mutation: E423Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Gene: lonA1, lon / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A059VAZ3, endopeptidase La
#2: Chemical
ChemComp-4KZ / N-[(1R)-1-(dihydroxyboranyl)-2-phenylethyl]-Nalpha-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide


Mass: 418.253 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H23BN4O4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 8.7
Details: 0.1 M Tris-HCl pH 8.7, 0.1 M CaCl2, 10-13% PEG 3350

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. all: 52050 / Num. obs: 45968 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Net I/av σ(I): 13.22 / Net I/σ(I): 0.168
Reflection shellResolution: 3.45→3.47 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.53 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data processing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPN, 1QZM and 1RR9

4ypn

1qzm

1rr9


Resolution: 3.45→30 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.841 / Cross valid method: THROUGHOUT / ESU R Free: 0.706 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 2447 5.1 %RANDOM
Rwork0.2372 ---
obs0.23859 45968 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.574 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2--1 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 3.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25091 0 267 0 25358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01925850
X-RAY DIFFRACTIONr_bond_other_d00.0225435
X-RAY DIFFRACTIONr_angle_refined_deg1.5172.00135058
X-RAY DIFFRACTIONr_angle_other_deg3.543358669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98453218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02523.951081
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.447154612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.29915210
X-RAY DIFFRACTIONr_chiral_restr0.0750.23981
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02128683
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025356
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_it2.7376.60912890
X-RAY DIFFRACTIONr_mcbond_other2.7376.60912889
X-RAY DIFFRACTIONr_mcangle_it4.6569.9116102
X-RAY DIFFRACTIONr_mcangle_other4.6569.9116103
X-RAY DIFFRACTIONr_scbond_it2.2446.84212959
X-RAY DIFFRACTIONr_scbond_other2.2446.84212960
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.02510.18518956
X-RAY DIFFRACTIONr_long_range_B_refined7.78855.65932316
X-RAY DIFFRACTIONr_long_range_B_other7.78855.65832317
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.45→3.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 105 -
Rwork0.299 1969 -
obs--55.78 %

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