[English] 日本語
Yorodumi
- PDB-4git: Crystal structure of alpha sub-domain of Lon protease from Brevib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4git
TitleCrystal structure of alpha sub-domain of Lon protease from Brevibacillus thermoruber
ComponentsLon protease
KeywordsHYDROLASE / DNA binding
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 / cytoplasm
Similarity search - Function
Lon protease, bacterial / 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, bacterial / 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) / Helicase, Ruva Protein; domain 3 - #60 / PUA-like superfamily / Helicase, Ruva Protein; domain 3 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBrevibacillus thermoruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.882 Å
AuthorsChen, Y.D. / Chang, Y.Y. / Hsu, C.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis for DNA-mediated allosteric regulation facilitated by the AAA(+) module of Lon protease.
Authors: Lee, A.Y. / Chen, Y.D. / Chang, Y.Y. / Lin, Y.C. / Chang, C.F. / Huang, S.J. / Wu, S.H. / Hsu, C.H.
History
DepositionAug 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lon protease
B: Lon protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8934
Polymers28,7012
Non-polymers1922
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-22 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.283, 94.283, 94.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

-
Components

#1: Protein Lon protease


Mass: 14350.596 Da / Num. of mol.: 2 / Fragment: alpha sub-domain, UNP RESIDUES 491-605
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus thermoruber (bacteria) / Strain: WR-249 / Gene: lon / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84FG5, endopeptidase La
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1M potassium phosphate, 0.2M sodium chloride, 12.5% PEG 8000, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 19, 2010
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.88→30 Å / Num. all: 6542 / Num. obs: 6542 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.88 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 38 / Num. unique all: 6523 / Rsym value: 0.504

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M6A

3m6a


Resolution: 2.882→29.815 Å / SU ML: 0.4 / σ(F): 1.38 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 643 9.84 %RANDOM
Rwork0.2013 ---
obs0.2061 6534 99.69 %-
all-6542 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.236 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.882→29.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 10 4 1506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091516
X-RAY DIFFRACTIONf_angle_d1.3172026
X-RAY DIFFRACTIONf_dihedral_angle_d16.262618
X-RAY DIFFRACTIONf_chiral_restr0.093224
X-RAY DIFFRACTIONf_plane_restr0.006258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8823-3.10460.3521320.29531161100
3.1046-3.41670.32391280.23521153100
3.4167-3.91010.28711290.20511170100
3.9101-4.92280.1951260.16971181100
4.9228-29.81650.22881280.1949122699
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)
17.6171.3485-1.42934.99453.06264.4360.26570.5872-0.03960.3977-0.2523-1.4304-1.33720.0214-0.93530.4441-0.1884-0.05090.64340.38180.642819.74-8.354141.793
26.86491.0239-4.05789.0528-3.47799.2070.31760.88360.35960.44250.0506-0.1056-0.2748-0.4871-0.16860.4555-0.06650.0830.60010.2180.270121.594-6.683131.589
36.27731.5715-3.79442.858-3.54975.03560.79010.66841.76830.77450.20391.1067-0.8139-1.3149-0.93250.8960.20240.11921.39850.22530.628521.684-10.769121.095
43.67670.0435-1.78527.3497-4.20164.18790.0866-0.4689-0.76371.3297-0.4307-0.3863-0.307-0.2969-0.47620.5692-0.4318-0.00890.69070.15760.38347.4678.367114.034
57.33613.2115-5.98546.4492-1.13836.16640.07930.7407-0.26890.5147-0.208-0.05250.2054-1.1351-0.12650.4549-0.18090.05470.64740.13850.427436.9646.941114.222
68.72360.72590.51186.4557-0.56155.9844-0.19060.5612-0.3273-0.8089-0.3642-1.27781.25430.02990.4820.4775-0.27360.25790.75850.03180.607139.1625.351123.023
74.313-0.5072-0.5240.65731.14262.02620.05952.8145-0.1575-0.4878-0.11280.40660.8794-0.95630.89420.7662-0.49390.18641.529-0.20770.760625.6029.591114.469
82.2552.37373.24623.61230.929120.53130.4821-3.33280.8865-0.2375-2.9022.5348-0.2188-0.52161.00380.3594-0.15971.1113-0.06511.851433.35817.718124.252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 492:503)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 504:548)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 549:582)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 492:503)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 504:540)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 541:548)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 549:577)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 578:582)

+
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