[English] 日本語
Yorodumi
- PDB-4ynn: Structure of Legionella pneumophila DegQ (S190A variant) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ynn
TitleStructure of Legionella pneumophila DegQ (S190A variant)
Components
  • Hepta-peptide
  • Hexa-peptide
  • Octapeptide
  • Protease DO
  • UNK-UNK-UNK
KeywordsHYDROLASE / Bacterial Proteins / Legionella / Models / Molecular / Peptide Hydrolases / Protein Conformation
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / periplasmic space / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase S1C, Do / PDZ domain / PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / Thrombin, subunit H - #120 / PDZ domain / Pdz3 Domain / PDZ domain profile. ...Peptidase S1C, Do / PDZ domain / PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / Thrombin, subunit H - #120 / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Thrombin, subunit H / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWrase, R. / Hilgenfeld, R. / Hansen, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationEXC 306 Germany
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structures of DegQ from Legionella pneumophila Define Distinct ON and OFF States.
Authors: Schubert, A. / Wrase, R. / Hilgenfeld, R. / Hansen, G.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease DO
B: Protease DO
C: Protease DO
D: Protease DO
E: Protease DO
F: Protease DO
G: Protease DO
H: Protease DO
I: Octapeptide
J: Hexa-peptide
K: Hepta-peptide
L: Hexa-peptide
M: Hepta-peptide
N: Hepta-peptide
O: Hepta-peptide
P: Hepta-peptide
Q: UNK-UNK-UNK
R: UNK-UNK-UNK
S: UNK-UNK-UNK
T: UNK-UNK-UNK
U: UNK-UNK-UNK
V: UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)387,51422
Polymers387,51422
Non-polymers00
Water00
1
A: Protease DO
D: Protease DO
G: Protease DO
H: Protease DO
I: Octapeptide
L: Hexa-peptide
O: Hepta-peptide
P: Hepta-peptide
Q: UNK-UNK-UNK
T: UNK-UNK-UNK
U: UNK-UNK-UNK
V: UNK-UNK-UNK

A: Protease DO
D: Protease DO
G: Protease DO
H: Protease DO
I: Octapeptide
L: Hexa-peptide
O: Hepta-peptide
P: Hepta-peptide
Q: UNK-UNK-UNK
T: UNK-UNK-UNK
U: UNK-UNK-UNK
V: UNK-UNK-UNK

A: Protease DO
D: Protease DO
G: Protease DO
H: Protease DO
I: Octapeptide
L: Hexa-peptide
O: Hepta-peptide
P: Hepta-peptide
Q: UNK-UNK-UNK
T: UNK-UNK-UNK
U: UNK-UNK-UNK
V: UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)582,21936
Polymers582,21936
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area64090 Å2
ΔGint-375 kcal/mol
Surface area191330 Å2
MethodPISA
2
B: Protease DO
C: Protease DO
E: Protease DO
F: Protease DO
J: Hexa-peptide
K: Hepta-peptide
M: Hepta-peptide
N: Hepta-peptide
R: UNK-UNK-UNK
S: UNK-UNK-UNK

B: Protease DO
C: Protease DO
E: Protease DO
F: Protease DO
J: Hexa-peptide
K: Hepta-peptide
M: Hepta-peptide
N: Hepta-peptide
R: UNK-UNK-UNK
S: UNK-UNK-UNK

B: Protease DO
C: Protease DO
E: Protease DO
F: Protease DO
J: Hexa-peptide
K: Hepta-peptide
M: Hepta-peptide
N: Hepta-peptide
R: UNK-UNK-UNK
S: UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)580,32330
Polymers580,32330
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area61980 Å2
ΔGint-367 kcal/mol
Surface area191430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.909, 147.909, 383.514
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein
Protease DO


Mass: 47631.133 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 31-466 / Mutation: S190A
Source method: isolated from a genetically manipulated source
Details: co-purified peptide fragment modelled as poly-Ala
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: htrA, lpg1331 / Plasmid: pQE-31 / Production host: Escherichia coli (E. coli) / Strain (production host): KU98
References: UniProt: Q5ZVV9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Octapeptide


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: co-purified peptide fragment modelled as poly-Ala / Source: (natural) Escherichia coli (E. coli)
#3: Protein/peptide Hexa-peptide


Mass: 528.644 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: co-purified peptide fragment modelled as poly-Ala / Source: (natural) Escherichia coli (E. coli)
#4: Protein/peptide
Hepta-peptide


Mass: 613.749 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: co-purified peptide fragment modelled as poly-Ala / Source: (natural) Escherichia coli (E. coli)
#5: Protein/peptide
UNK-UNK-UNK


Mass: 273.330 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: co-purified peptide fragment modelled as poly-Ala / Source: (natural) Escherichia coli (E. coli)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 100 mM citrate pH5.5; 17.5% (w/v) PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→28.543 Å / Num. obs: 77028 / % possible obs: 98.99 % / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.5
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.1 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PV2

3pv2


Resolution: 3.2→28.543 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 3873 5.03 %
Rwork0.181 --
obs0.183 77028 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→28.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24195 0 0 0 24195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424565
X-RAY DIFFRACTIONf_angle_d0.86233270
X-RAY DIFFRACTIONf_dihedral_angle_d14.3389029
X-RAY DIFFRACTIONf_chiral_restr0.0584016
X-RAY DIFFRACTIONf_plane_restr0.0054327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.2390.30161080.28082337X-RAY DIFFRACTION88
3.239-3.27990.30011140.28962447X-RAY DIFFRACTION92
3.2799-3.3230.37351190.29882565X-RAY DIFFRACTION98
3.323-3.36850.29631590.26792646X-RAY DIFFRACTION100
3.3685-3.41650.28521310.24032602X-RAY DIFFRACTION100
3.4165-3.46740.2591340.24282627X-RAY DIFFRACTION100
3.4674-3.52150.29861120.23582686X-RAY DIFFRACTION100
3.5215-3.57910.26051570.21722577X-RAY DIFFRACTION100
3.5791-3.64070.2671350.21492607X-RAY DIFFRACTION100
3.6407-3.70680.24241520.22362668X-RAY DIFFRACTION100
3.7068-3.77790.26721680.23042597X-RAY DIFFRACTION100
3.7779-3.85490.23661190.20892602X-RAY DIFFRACTION100
3.8549-3.93850.26951360.19962647X-RAY DIFFRACTION100
3.9385-4.02990.25921280.20052641X-RAY DIFFRACTION100
4.0299-4.13030.2281330.18342643X-RAY DIFFRACTION100
4.1303-4.24170.21661570.16322620X-RAY DIFFRACTION100
4.2417-4.36610.18081280.15292630X-RAY DIFFRACTION100
4.3661-4.50650.20011530.1452620X-RAY DIFFRACTION100
4.5065-4.66690.18431560.13582609X-RAY DIFFRACTION100
4.6669-4.85290.20841200.14442659X-RAY DIFFRACTION100
4.8529-5.07250.18521450.14092639X-RAY DIFFRACTION100
5.0725-5.33830.15371490.15232627X-RAY DIFFRACTION100
5.3383-5.67040.22581570.17262612X-RAY DIFFRACTION100
5.6704-6.10420.21461250.17122662X-RAY DIFFRACTION100
6.1042-6.71130.19851430.16292656X-RAY DIFFRACTION100
6.7113-7.66590.20351400.17412621X-RAY DIFFRACTION100
7.6659-9.59690.16921490.14172650X-RAY DIFFRACTION100
9.5969-28.54420.17261460.14922658X-RAY DIFFRACTION99

+
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