[English] 日本語
Yorodumi
- PDB-6z5q: The RSL - sulfonato-calix[8]arene complex, P3 form, acetate pH 4.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z5q
TitleThe RSL - sulfonato-calix[8]arene complex, P3 form, acetate pH 4.0
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / calixarene / protein framework / cage / crystal engineering / molecular glue / synthetic receptor / macrocycle / biomaterial
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Lipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-D-fructopyranose / sulfonato-calix[8]arene / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsRamberg, K. / Engilberge, S. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Facile Fabrication of Protein-Macrocycle Frameworks.
Authors: Ramberg, K.O. / Engilberge, S. / Skorek, T. / Crowley, P.B.
History
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,53512
Polymers19,4672
Non-polymers4,06810
Water7,692427
1
A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,30318
Polymers29,2013
Non-polymers6,10215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8200 Å2
ΔGint-16 kcal/mol
Surface area13670 Å2
MethodPISA
2
B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,30318
Polymers29,2013
Non-polymers6,10215
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 area8060 Å2
ΔGint-13 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.851, 59.851, 64.631
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

21A-379-

HOH

31B-353-

HOH

41B-380-

HOH

51B-413-

HOH

-
Components

#1: Protein Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 9733.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: Chemical ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar
ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.29 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 4
Details: 0.02 M sodium acetate, 0.05 M NaCl, 0.01 M sulfonato-calix[8]arene, 0.005 M D-fructose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.29→51.83 Å / Num. obs: 64914 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Rrim(I) all: 0.078 / Net I/σ(I): 13.5
Reflection shellResolution: 1.29→1.32 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3257 / CC1/2: 0.951 / Rpim(I) all: 0.222 / Rrim(I) all: 0.689 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 1.29→51.83 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.35 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1649 3377 5.21 %
Rwork0.1364 61468 -
obs0.1379 64845 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.44 Å2 / Biso mean: 21.2167 Å2 / Biso min: 10.62 Å2
Refinement stepCycle: final / Resolution: 1.29→51.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 264 430 2068
Biso mean--22.53 34.13 -
Num. residues----180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.29-1.310.26411380.204425842722
1.31-1.330.207860.183926222708
1.33-1.350.20281120.171925262638
1.35-1.370.17491530.157925942747
1.37-1.40.17731460.148425172663
1.4-1.420.20311800.147325782758
1.42-1.450.19551220.139625572679
1.45-1.480.14351340.138725532687
1.48-1.510.2111000.136325912691
1.51-1.550.16291880.128625592747
1.55-1.590.20751080.130225732681
1.59-1.630.1571440.129225542698
1.63-1.680.13021240.128825912715
1.68-1.730.18091460.126725362682
1.73-1.790.1411680.133825272695
1.79-1.860.16131300.132225812711
1.86-1.950.18131200.137825832703
1.95-2.050.16691590.137725412700
2.05-2.180.18431960.137124782674
2.18-2.350.15621400.142425722712
2.35-2.580.14381680.139925692737
2.58-2.960.15591640.139925222686
2.96-3.720.15921250.129825772702
3.72-27.420.1631260.126525832709

+
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