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- PDB-6ihg: N terminal domain of Mycobacterium avium complex Lon protease -

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Basic information

Entry
Database: PDB / ID: 6ihg
TitleN terminal domain of Mycobacterium avium complex Lon protease
ComponentsLon proteaseLon protease family
KeywordsHYDROLASE / Lon N-domain / ATP dependent
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 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 N-terminal domain profile. / Lon protease, N-terminal domain ...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 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 speciesMycobacterium [tuberculosis] TKK-01-0051 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.397 Å
AuthorsChen, X.Y. / Zhang, S.J. / Bi, F.K. / Guo, C.Y. / Yao, H.W. / Lin, D.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China2016YFA0500600 China
CitationJournal: Protein Sci. / Year: 2019
Title: Crystal structure of the N domain of Lon protease from Mycobacterium avium complex.
Authors: Chen, X. / Zhang, S. / Bi, F. / Guo, C. / Feng, L. / Wang, H. / Yao, H. / Lin, D.
History
DepositionSep 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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


Theoretical massNumber of molelcules
Total (without water)20,9221
Polymers20,9221
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.631, 58.631, 118.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 20921.736 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium [tuberculosis] TKK-01-0051 (bacteria)
Gene: lon, K875_02975 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A051TYQ1, endopeptidase La
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 295 K / Method: liquid diffusion / Details: Sodium formate,Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.397→50 Å / Num. obs: 8942 / % possible obs: 91.81 % / Redundancy: 18.3 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 3
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.63 / Num. unique obs: 457 / CC1/2: 0.968 / Rsym value: 0.63

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Processing

Software
NameVersionClassification
PHENIX(1.15rc2_3428: ???)refinement
PHASERphasing
PHENIXmodel building
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD
Starting model: 6IHF

6ihf
PDB Unreleased entry


Resolution: 2.397→24.823 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 475 5.31 %
Rwork0.2274 --
obs0.2296 8942 91.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.397→24.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 0 28 1437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091430
X-RAY DIFFRACTIONf_angle_d1.0911949
X-RAY DIFFRACTIONf_dihedral_angle_d3.982870
X-RAY DIFFRACTIONf_chiral_restr0.056236
X-RAY DIFFRACTIONf_plane_restr0.005251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3974-2.74390.37781340.32922273X-RAY DIFFRACTION76
2.7439-3.45550.3331630.26093040X-RAY DIFFRACTION100
3.4555-24.82390.21331780.18633154X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.4615 Å / Origin y: 26.2422 Å / Origin z: 13.2043 Å
111213212223313233
T0.1938 Å20.0243 Å2-0.0056 Å2-0.2072 Å2-0.0422 Å2--0.2102 Å2
L1.2707 °2-0.3525 °2-0.1861 °2-1.3257 °20.0413 °2--6.2317 °2
S0.1389 Å °-0.0592 Å °-0.1422 Å °0.0792 Å °0.0229 Å °-0.0246 Å °-0.0939 Å °-0.3031 Å °-0.0861 Å °
Refinement TLS groupSelection details: (chain A and resseq 5:190)

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