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- PDB-7euy: Crystal structure of the Lon-like protease MtaLonC with D582A mut... -

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Basic information

Entry
Database: PDB / ID: 7euy
TitleCrystal structure of the Lon-like protease MtaLonC with D582A mutation in complex with substrate polypeptide
Components
  • ALA-PRO-GLU-ALA-VAL
  • Endopeptidase La
KeywordsHYDROLASE / protease / TTC1975 peptidase / Lon-like protease
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / ATP binding
Similarity search - Function
Lon protease, AAA domain / LonB-like, AAA domain / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon proteolytic domain profile. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Endopeptidase La
Similarity search - Component
Biological speciesMeiothermus taiwanensis (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHsieh, K.Y. / Kuo, C.I. / Su, S.C. / Huang, K.F. / Chang, C.I.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2320-B-001-011-MY3 Taiwan
Academia Sinica (Taiwan) Taiwan
CitationJournal: Sci Adv / Year: 2021
Title: Processive cleavage of substrate at individual proteolytic active sites of the Lon protease complex.
Authors: Shanshan Li / Kan-Yen Hsieh / Chiao-I Kuo / Shih-Chieh Su / Kai-Fa Huang / Kaiming Zhang / Chung-I Chang /
Abstract: [Figure: see text].
History
DepositionMay 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endopeptidase La
S: ALA-PRO-GLU-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1233
Polymers81,0282
Non-polymers951
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-12 kcal/mol
Surface area27790 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)115.838, 115.838, 135.455
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-970-

HOH

21A-991-

HOH

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Components

#1: Protein Endopeptidase La /


Mass: 80542.352 Da / Num. of mol.: 1 / Mutation: S582A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C9DRU9, endopeptidase La
#2: Protein/peptide ALA-PRO-GLU-ALA-VAL


Mass: 485.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10% isopropanol, 100 mM monosodium phosphate and 100 mM sodium citrate at pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jun 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 52084 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 26.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5127 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FW9
Resolution: 2.2→33.46 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.707 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 2655 5.1 %RANDOM
Rwork0.1824 ---
obs0.1839 49382 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.07 Å2 / Biso mean: 44.514 Å2 / Biso min: 20.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-1.14 Å20 Å2
2---1.14 Å20 Å2
3---3.7 Å2
Refinement stepCycle: final / Resolution: 2.2→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 5 280 4829
Biso mean--33.17 48.13 -
Num. residues----592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194638
X-RAY DIFFRACTIONr_bond_other_d0.0010.024500
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9846300
X-RAY DIFFRACTIONr_angle_other_deg0.864310312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62422.885208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50915742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5141548
X-RAY DIFFRACTIONr_chiral_restr0.0930.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021048
LS refinement shellResolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 198 -
Rwork0.22 3591 -
all-3789 -
obs--98.8 %

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