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- PDB-7ev6: Crystal structure of the Lon-like protease MtaLonC with D581A mut... -

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Basic information

Entry
Database: PDB / ID: 7ev6
TitleCrystal structure of the Lon-like protease MtaLonC with D581A mutation in complex with F-b20-Q
Components
  • Endopeptidase La
  • F-b20-Q peptide {ortho-aminobenzoic acid (Abz)- QLRSLNGEWRFAWFPAPEAV[Tyr(3-NO2)]A}
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: 2.1 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 20, 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: F-b20-Q peptide {ortho-aminobenzoic acid (Abz)- QLRSLNGEWRFAWFPAPEAV[Tyr(3-NO2)]A}
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2063
Polymers81,1112
Non-polymers951
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-11 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)115.826, 115.826, 136.256
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-995-

HOH

21A-1008-

HOH

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Components

#1: Protein Endopeptidase La /


Mass: 80514.344 Da / Num. of mol.: 1
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 F-b20-Q peptide {ortho-aminobenzoic acid (Abz)- QLRSLNGEWRFAWFPAPEAV[Tyr(3-NO2)]A}


Mass: 596.586 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.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10% isopropanol, 100mM monosodium phosphate, 100mM sodium citrate

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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 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 57412 / % possible obs: 95.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.8
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 48926 / % possible all: 90.9

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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: 2.1→19.85 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.201 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2600 5 %RANDOM
Rwork0.154 ---
obs0.156 48926 85.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.74 Å2 / Biso mean: 32.65 Å2 / Biso min: 8.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2---1.05 Å20 Å2
3---2.1 Å2
Refinement stepCycle: final / Resolution: 2.1→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4602 0 5 427 5034
Biso mean--24.54 39.46 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194703
X-RAY DIFFRACTIONr_bond_other_d0.0010.024563
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9876389
X-RAY DIFFRACTIONr_angle_other_deg0.7913.00110452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.322.905210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02815752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1641548
X-RAY DIFFRACTIONr_chiral_restr0.0730.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021067
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 108 -
Rwork0.227 1896 -
all-2004 -
obs--45.26 %

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