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- PDB-7cra: Crystal structure of the N-terminal fragment (residue 1-291) of L... -

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Basic information

Entry
Database: PDB / ID: 7cra
TitleCrystal structure of the N-terminal fragment (residue 1-291) of LonA protease from Meiothermus taiwanensis
ComponentsLon proteaseLon protease family
KeywordsHYDROLASE / Lon protease / AAA+ protein
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
Biological speciesMeiothermus taiwanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLin, C.-C. / Chang, C.-I.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)105-2320-B-001-015-MY3 Taiwan
CitationJournal: Elife / Year: 2021
Title: Molecular insights into substrate recognition and discrimination by the N-terminal domain of Lon AAA+ protease.
Authors: Tzeng, S.R. / Tseng, Y.C. / Lin, C.C. / Hsu, C.Y. / Huang, S.J. / Kuo, Y.T. / Chang, C.I.
History
DepositionAug 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5623
Polymers33,3701
Non-polymers1922
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-16 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.016, 86.016, 110.126
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 33370.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Gene: lonA1, lon / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A059VAZ3, endopeptidase La
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.76 Å3/Da / Density % sol: 30.2 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 5.8 / Details: 0.1 M MES (pH 5.8) and 0.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Feb 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 27083 / % possible obs: 100 % / Redundancy: 20.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 49.1
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.779 / Num. unique obs: 2632

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CR9

7cr9


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.974 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 1391 5.1 %RANDOM
Rwork0.1841 ---
obs0.186 25692 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.04 Å2 / Biso mean: 17.006 Å2 / Biso min: 4.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 10 244 1938
Biso mean--27.44 28.21 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191722
X-RAY DIFFRACTIONr_bond_other_d0.0020.021703
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9912339
X-RAY DIFFRACTIONr_angle_other_deg0.75333910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01923.29179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39915306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3811518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 87 -
Rwork0.231 1853 -
all-1940 -
obs--99.44 %

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