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- PDB-7eux: Crystal structure of the Lon-like protease MtaLonC with D581A mut... -

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Database: PDB / ID: 7eux
TitleCrystal structure of the Lon-like protease MtaLonC with D581A mutation in complex with substrate polypeptide
  • 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)
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].
DepositionMay 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release

Structure visualization

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Deposited unit
A: Endopeptidase La
hetero molecules

Theoretical massNumber of molelcules
Total (without water)81,0953

  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-11 kcal/mol
Surface area27830 Å2
Unit cell
Length a, b, c (Å)115.742, 115.742, 135.998
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions



#1: Protein Endopeptidase La /

Mass: 80514.344 Da / Num. of mol.: 1 / Mutation: D581A
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
Details: b19, a known peptide substrate of Lon derived from an internal segment of beta-galactosidase, and F-b20-Q.
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.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10% isopropanol, 100 mM monosodium phosphate, 100 mM sodium citrate at pH 4.6.

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
Reflection twin
11H, K, L10.512
11K, H, -L20.488
ReflectionResolution: 2.25→20 Å / Num. obs: 48531 / % possible obs: 99.2 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 23.7
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4799 / % possible all: 98.2


PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FW9
Resolution: 2.25→19.83 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.841 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2255 5.2 %RANDOM
Rwork0.153 ---
obs0.155 41112 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.38 Å2 / Biso mean: 36.44 Å2 / Biso min: 14.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.46 Å2
Refinement stepCycle: final / Resolution: 2.25→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 5 257 4804
Biso mean--29.53 39.94 -
Num. residues----592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194637
X-RAY DIFFRACTIONr_bond_other_d0.0010.024500
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9856299
X-RAY DIFFRACTIONr_angle_other_deg0.797310312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19922.85207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69615742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1511548
X-RAY DIFFRACTIONr_chiral_restr0.0770.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021048
X-RAY DIFFRACTIONr_nbd_refined
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 105 -
Rwork0.206 1662 -
all-1767 -
obs--48.53 %

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