[English] 日本語
Yorodumi
- PDB-7cr9: Crystal structure of the N-terminal fragment (residue 1-206) of L... -

+
Open data


ID or keywords:

Loading...

-
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 / identical protein binding / metal ion 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more