[English] 日本語
Yorodumi
- PDB-4zpx: Crystal structure of Lon ATPase domain from Thermococcus onnurine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zpx
TitleCrystal structure of Lon ATPase domain from Thermococcus onnurineus NA1
ComponentsATP-dependent protease Lon
KeywordsHYDROLASE / AAA+ proteins / PS-1 insert / H2 insert / Ins1 / Lon Protease / Thermococcus onnurineus NA1 / ATP-independent proteolytic activity
Function / homology
Function and homology information


ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / regulation of DNA-templated transcription / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
Lon protease, archaeal / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain ...Lon protease, archaeal / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S5 domain 2-type fold, subgroup / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Archaeal Lon protease
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsAn, Y.J. / Kim, M.I. / Na, J.H. / Cha, S.S.
CitationJournal: To Be Published
Title: Structural disparity classifies AAA+ modules of Lon proteases into two distinct clades
Authors: Kim, M.I. / An, Y.J. / Na, J.H. / Cha, S.S.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent protease Lon
B: ATP-dependent protease Lon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0513
Polymers91,9592
Non-polymers921
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-0 kcal/mol
Surface area29490 Å2
Unit cell
Length a, b, c (Å)40.620, 61.599, 76.321
Angle α, β, γ (deg.)74.61, 87.11, 83.45
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein ATP-dependent protease Lon


Mass: 45979.539 Da / Num. of mol.: 2 / Fragment: UNP residues 1-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0529 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YU74
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.2M Potassium chloride, 0.01M Magnesium acetate, 0.05M tri-sodium citrate dihydrate pH 4.5, 12% PEG 4000, 5% n-Dodecyl-beta-D-maltoside

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 42270 / % possible obs: 93.1 % / Redundancy: 2.3 % / Net I/σ(I): 23.03

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→41.14 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.799 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 2130 5 %RANDOM
Rwork0.18157 ---
obs0.18444 40140 92.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.085 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å21.91 Å2-0.52 Å2
2---0.52 Å2-0.44 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.03→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4960 0 6 243 5209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195038
X-RAY DIFFRACTIONr_bond_other_d0.0010.025076
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.986815
X-RAY DIFFRACTIONr_angle_other_deg0.9233.00111647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89823.695203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91715882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1091542
X-RAY DIFFRACTIONr_chiral_restr0.1190.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215649
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021049
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_mcbond_it2.8973.1592625
X-RAY DIFFRACTIONr_mcbond_other2.8973.1572624
X-RAY DIFFRACTIONr_mcangle_it4.2534.7073269
X-RAY DIFFRACTIONr_mcangle_other4.2534.7093270
X-RAY DIFFRACTIONr_scbond_it3.7663.5822413
X-RAY DIFFRACTIONr_scbond_other3.7643.5822413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7495.2013547
X-RAY DIFFRACTIONr_long_range_B_refined8.13429.59921269
X-RAY DIFFRACTIONr_long_range_B_other8.12329.58221178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.035→2.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 133 -
Rwork0.227 2515 -
obs--79.81 %

+
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