[English] 日本語
Yorodumi
- PDB-7co3: HtrA-type protease AlgWS227A with tripeptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7co3
TitleHtrA-type protease AlgWS227A with tripeptide
Components
  • AlgW protein
  • TRP-VAL-PHE
KeywordsPEPTIDE BINDING PROTEIN / complex
Function / homology
Function and homology information


peptidase activity / serine-type endopeptidase activity / proteolysis
Similarity search - Function
: / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, T. / Song, Y.J. / Bao, R.
CitationJournal: Mbio / Year: 2021
Title: Molecular Basis of the Versatile Regulatory Mechanism of HtrA-Type Protease AlgW from Pseudomonas aeruginosa.
Authors: Li, T. / Song, Y. / Luo, L. / Zhao, N. / He, L. / Kang, M. / Li, C. / Zhu, Y. / Shen, Y. / Zhao, C. / Yang, J. / Huang, Q. / Mou, X. / Zong, Z. / Yang, J. / Tang, H. / He, Y. / Bao, R.
History
DepositionAug 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: TRP-VAL-PHE
A: AlgW protein


Theoretical massNumber of molelcules
Total (without water)41,4732
Polymers41,4732
Non-polymers00
Water2,972165
1
C: TRP-VAL-PHE
A: AlgW protein

C: TRP-VAL-PHE
A: AlgW protein

C: TRP-VAL-PHE
A: AlgW protein


Theoretical massNumber of molelcules
Total (without water)124,4206
Polymers124,4206
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7630 Å2
ΔGint-47 kcal/mol
Surface area38510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.614, 96.614, 119.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21A-483-

HOH

31A-534-

HOH

41A-538-

HOH

51A-547-

HOH

61A-555-

HOH

71A-561-

HOH

81A-564-

HOH

-
Components

#1: Protein/peptide TRP-VAL-PHE


Mass: 450.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein AlgW protein


Mass: 41022.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: algW, PA4446 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HVX1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.8M Sodium/Potassium Phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.898→39.49 Å / Num. obs: 49248 / % possible obs: 99.82 % / Redundancy: 28.5 % / Biso Wilson estimate: 25.71 Å2 / CC1/2: 0.958 / Net I/σ(I): 24.67
Reflection shellResolution: 1.898→1.996 Å / Num. unique obs: 2558 / CC1/2: 0.915

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SOZ

1soz


Resolution: 1.9→39.49 Å / SU ML: 0.3098 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.815 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2695 3706 7.53 %
Rwork0.2335 45542 -
obs0.2362 49248 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 25 165 2371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332231
X-RAY DIFFRACTIONf_angle_d1.50263026
X-RAY DIFFRACTIONf_chiral_restr0.0881363
X-RAY DIFFRACTIONf_plane_restr0.0083398
X-RAY DIFFRACTIONf_dihedral_angle_d13.84851337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.39551400.37331676X-RAY DIFFRACTION95.43
1.92-1.950.33831390.33831717X-RAY DIFFRACTION99.95
1.95-1.980.31581490.33771782X-RAY DIFFRACTION100
1.98-2.010.37931370.33311723X-RAY DIFFRACTION100
2.01-2.040.34311440.32621751X-RAY DIFFRACTION100
2.04-2.070.38951460.33171759X-RAY DIFFRACTION100
2.07-2.110.3511440.30741770X-RAY DIFFRACTION100
2.11-2.150.32251420.29281770X-RAY DIFFRACTION100
2.15-2.190.30411410.27431758X-RAY DIFFRACTION100
2.19-2.230.27811460.26911722X-RAY DIFFRACTION100
2.23-2.280.281440.25431747X-RAY DIFFRACTION100
2.28-2.330.29651470.24551764X-RAY DIFFRACTION100
2.33-2.390.28921430.25161779X-RAY DIFFRACTION100
2.39-2.460.30291450.24991729X-RAY DIFFRACTION100
2.46-2.530.2771400.22891765X-RAY DIFFRACTION100
2.53-2.610.2611460.24541768X-RAY DIFFRACTION100
2.61-2.70.28841420.22581739X-RAY DIFFRACTION100
2.7-2.810.28381440.22021736X-RAY DIFFRACTION100
2.81-2.940.28941370.231786X-RAY DIFFRACTION100
2.94-3.090.30611430.23161732X-RAY DIFFRACTION100
3.09-3.290.25971420.231768X-RAY DIFFRACTION100
3.29-3.540.21611460.20641753X-RAY DIFFRACTION100
3.54-3.90.22611400.19581747X-RAY DIFFRACTION100
3.9-4.460.22771490.1751752X-RAY DIFFRACTION100
4.46-5.620.22641330.19761771X-RAY DIFFRACTION100
5.62-39.490.24721370.21521778X-RAY DIFFRACTION99.95

+
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