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- PDB-7cr9: Crystal structure of the N-terminal fragment (residue 1-206) of L... -

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Basic information

Entry
Database: PDB / ID: 7cr9
TitleCrystal structure of the N-terminal fragment (residue 1-206) of LonA protease from Meiothermus taiwanensis
ComponentsLon protease
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 / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Lon protease, bacterial / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Lon protease, bacterial / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / 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, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Roll / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMeiothermus taiwanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 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 12, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lon protease
B: Lon protease


Theoretical massNumber of molelcules
Total (without water)46,8942
Polymers46,8942
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.830, 58.296, 198.492
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 or resid 2 through 31...
21(chain B and (resid 0 or resid 2 through 31...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS(chain A and (resid 0 or resid 2 through 31...AA01
12ARGARGLYSLYS(chain A and (resid 0 or resid 2 through 31...AA2 - 313 - 32
13ALAALAALAALA(chain A and (resid 0 or resid 2 through 31...AA33 - 7434 - 75
14HISHISASPASP(chain A and (resid 0 or resid 2 through 31...AA0 - 2061 - 207
15PROPROPROPRO(chain A and (resid 0 or resid 2 through 31...AA115116
16METMETMETMET(chain A and (resid 0 or resid 2 through 31...AA12
17HISHISASPASP(chain A and (resid 0 or resid 2 through 31...AA0 - 2061 - 207
18HISHISASPASP(chain A and (resid 0 or resid 2 through 31...AA0 - 2061 - 207
19HISHISLEULEU(chain A and (resid 0 or resid 2 through 31...AA0 - 1421 - 143
110LEULEUASPASP(chain A and (resid 0 or resid 2 through 31...AA144 - 206145 - 207
21HISHISHISHIS(chain B and (resid 0 or resid 2 through 31...BB01
22ARGARGLYSLYS(chain B and (resid 0 or resid 2 through 31...BB2 - 313 - 32
23ALAALAALAALA(chain B and (resid 0 or resid 2 through 31...BB33 - 7434 - 75
24LEULEUALAALA(chain B and (resid 0 or resid 2 through 31...BB77 - 8878 - 89
25ALAALAGLUGLU(chain B and (resid 0 or resid 2 through 31...BB90 - 11291 - 113
26PROPROPROPRO(chain B and (resid 0 or resid 2 through 31...BB115116
27ASPASPVALVAL(chain B and (resid 0 or resid 2 through 31...BB117 - 121118 - 122
28VALVALHISHIS(chain B and (resid 0 or resid 2 through 31...BB123 - 139124 - 140
29SERSERLEULEU(chain B and (resid 0 or resid 2 through 31...BB141 - 142142 - 143
210LEULEUASPASP(chain B and (resid 0 or resid 2 through 31...BB144 - 206145 - 207

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Components

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


Mass: 23446.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Gene: lonA1, lon / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059VAZ3, endopeptidase La
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7.5
Details: 0.1 M Tris-HCl (pH 7.5), 0.2 M Sodium acetate and 30% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.09→30 Å / Num. obs: 23209 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 17.95
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.937 / Num. unique obs: 2198 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M65

3m65


Resolution: 2.095→29.411 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1193 5.14 %
Rwork0.2093 22013 -
obs0.2114 23206 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.42 Å2 / Biso mean: 53.1257 Å2 / Biso min: 19.85 Å2
Refinement stepCycle: final / Resolution: 2.095→29.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 0 107 3392
Biso mean---52.66 -
Num. residues----413
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1140X-RAY DIFFRACTION5.835TORSIONAL
12B1140X-RAY DIFFRACTION5.835TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0951-2.1790.30731430.2542231697
2.179-2.27810.27251340.23372381100
2.2781-2.39820.2941160.22892433100
2.3982-2.54840.23221320.21152448100
2.5484-2.7450.25161310.22542444100
2.745-3.0210.26841230.22712451100
3.021-3.45750.28621230.21262455100
3.4575-4.35390.22381440.19272499100
4.3539-29.4110.23411470.1981258697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.89180.665-0.0624.5724-1.34252.8768-0.0020.03350.1714-0.0307-0.01050.0298-0.1395-0.0520.03150.16010.0301-0.01850.2308-0.01110.1865-9.1541-8.342912.2663
21.9048-1.40861.2324.7822-2.14943.41020.0693-0.1769-0.07310.03820.0452-0.10110.1548-0.0301-0.10340.1951-0.0447-0.03270.281-0.00250.2386-4.32868.234836.8544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 0:206)A0 - 206
2X-RAY DIFFRACTION2(chain B and resseq 0:206)B0 - 206

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