[English] 日本語
Yorodumi
- PDB-8rqp: In meso structure of the alginate exporter, AlgE, from Pseudomona... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rqp
TitleIn meso structure of the alginate exporter, AlgE, from Pseudomonas aeruginosa in 7.10 monoacylglycerol
ComponentsAlginate production protein AlgE
KeywordsMEMBRANE PROTEIN / Alginate exporter
Function / homologyAlginate export domain / Alginate export / alginic acid biosynthetic process / cell outer membrane / : / : / CITRIC ACID / Alginate production protein AlgE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSmithers, L. / Boland, C. / Krawinski, P. / Caffrey, M.
Funding support Ireland, 4items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
Science Foundation Ireland22/FFP-A/10278 Ireland
Irish Research CouncilGOIPG/2019/3074 Ireland
Irish Research CouncilGOIPD/2021/40 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2024
Title: 7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins.
Authors: Krawinski, P. / Smithers, L. / van Dalsen, L. / Boland, C. / Ostrovitsa, N. / Perez, J. / Caffrey, M.
History
DepositionJan 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alginate production protein AlgE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,37020
Polymers53,5021
Non-polymers4,86819
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-38 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.358, 74.546, 115.913
Angle α, β, γ (deg.)90.000, 102.490, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Alginate production protein AlgE


Mass: 53502.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: algE, alg76, PA3544 / Production host: Escherichia coli (E. coli) / References: UniProt: P18895

-
Non-polymers , 9 types, 253 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-A1H2K / 7.10 monoacylglycerol (S-form) / [(2S)-2,3-bis(oxidanyl)propyl] (E)-heptadec-7-enoate


Mass: 342.513 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C20H38O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-A1H52 / 7.10 monoacylglycerol (R-form) / [(2R)-2,3-bis(oxidanyl)propyl] (E)-heptadec-7-enoate


Mass: 342.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H38O4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 34-41 %(v/v) PEG400, 100 mM LiSO4, and 100 mM Na-Citrate at pH 5.6 and 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9779 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.45→39.4 Å / Num. obs: 61350 / % possible obs: 90.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 15.48 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.2
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 3068 / CC1/2: 0.273

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→39.37 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8835
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 3103 5.07 %
Rwork0.1898 58151 -
obs0.1915 61254 72.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.46 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 304 234 4173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01244085
X-RAY DIFFRACTIONf_angle_d1.27255464
X-RAY DIFFRACTIONf_chiral_restr0.257534
X-RAY DIFFRACTIONf_plane_restr0.0118706
X-RAY DIFFRACTIONf_dihedral_angle_d15.7305740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.407610.288570X-RAY DIFFRACTION1.81
1.47-1.490.2941100.242153X-RAY DIFFRACTION4.38
1.49-1.520.2592240.255288X-RAY DIFFRACTION8.17
1.52-1.550.2998350.2544572X-RAY DIFFRACTION15.96
1.55-1.580.3116560.2642983X-RAY DIFFRACTION27.38
1.58-1.610.2639870.25981629X-RAY DIFFRACTION44.14
1.61-1.640.30791370.27152292X-RAY DIFFRACTION64.07
1.64-1.680.2741570.25662858X-RAY DIFFRACTION77.67
1.68-1.730.29211500.25383100X-RAY DIFFRACTION85.26
1.73-1.770.29381550.24863215X-RAY DIFFRACTION88.2
1.77-1.820.34061570.23813391X-RAY DIFFRACTION92.06
1.82-1.880.24882020.21793416X-RAY DIFFRACTION93.71
1.88-1.950.24922040.20083433X-RAY DIFFRACTION94.59
1.95-2.030.19881860.18833490X-RAY DIFFRACTION95.8
2.03-2.120.21871970.17683641X-RAY DIFFRACTION99.71
2.12-2.230.21541890.17523669X-RAY DIFFRACTION99.92
2.23-2.370.21421870.17273642X-RAY DIFFRACTION99.97
2.37-2.560.19321810.17793664X-RAY DIFFRACTION99.79
2.56-2.810.22581880.19183662X-RAY DIFFRACTION99.72
2.81-3.220.23422040.18183645X-RAY DIFFRACTION99.12
3.22-4.060.17892150.16123569X-RAY DIFFRACTION97.58
4.06-39.370.21761810.18633769X-RAY DIFFRACTION99.67
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)
10.9494355865260.1822352474490.01143413430593.97495562187-3.453822300693.049804939880.01362524198890.0571278019268-0.0253324202884-0.0717418211064-0.0120434609012-0.02571964307720.0818447682735-0.00129054417806-0.01770559919320.110504775593-0.02201161864810.003463480591440.110157434828-0.05969023603090.1218744817785.79160536573-4.6162391912438.5461047143
22.07285023082-1.645623467590.8649317543222.82705656753-0.9858308924670.946253833840.1162229132880.1515058055930.121435608719-0.219741739181-0.188812822503-0.0717383351163-0.03594892852160.162526140810.09795334912220.0812415128543-0.0339871125199-0.02268157883210.132135778039-0.004918815479450.1172016802583.66816734871-10.546097657332.0454405709
31.300480338940.107388463279-0.008147079268720.74605277935-0.09830098469230.6826858808060.0269435394612-0.02354202147750.05069098809090.0557323815223-0.00922873874581-0.0101982795727-0.04091498972670.0470964807856-0.005932918166240.0641277818401-0.0116585004681-0.005136899137850.0518272745251-0.003416537212650.077274252992120.7371568594-13.5341131533.843174359
40.5470751665850.189177034217-0.2079346356481.484355581981.361676264452.010228956180.01542732282690.0828039650555-0.00922416061971-0.0684122307947-0.1100105260970.01035878979280.0122117353488-0.2179870302260.1007708591640.0517911096789-0.0136584517784-0.001006257428790.1137274962020.008396438223080.083710151707325.3583114434-1.8134239951522.1102927248
51.9825126625-0.327340438066-1.352356412261.168007421270.6002837731973.392712286540.01589628753570.03346626450450.000460039672449-0.121237039352-0.07338218554830.04611701148730.003780736515410.0212079871940.04021730489830.0620198386579-0.0191968297851-0.02381491169360.0628836449614-0.005437291716920.12522352739817.99058007948.5967548519427.7130966071
62.157470773581.32313737302-2.149609197972.4421701524-1.625428072572.238477658180.02715140540020.01432526878480.145464098673-0.03678674356690.009593486702260.0917632774920.0348965335680.00414166215035-0.07230837027970.0731374756909-0.00792455314147-0.04898954818210.113665641475-0.007737082261310.1341230502647.012095421138.3564125249132.3963561978
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 65 )13 - 651 - 53
22chain 'A' and (resid 66 through 123 )66 - 12354 - 102
33chain 'A' and (resid 124 through 230 )124 - 230103 - 209
44chain 'A' and (resid 231 through 350 )231 - 350210 - 329
55chain 'A' and (resid 351 through 424 )351 - 424330 - 403
66chain 'A' and (resid 425 through 490 )425 - 490404 - 459

+
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://pdbjlvh1.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