[English] 日本語
Yorodumi
- PDB-7t7z: The crystal structure of family 8 carbohydrate-binding module fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t7z
TitleThe crystal structure of family 8 carbohydrate-binding module from Dictyostelium discoideum
ComponentsEndoglucanaseCellulase
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-binding protein / ligand specificity / cellulose / CAZymes
Function / homology
Function and homology information


spore germination / cellulose binding / cellulase / sporulation resulting in formation of a cellular spore / cellulase activity / cellulose catabolic process / extracellular region
Similarity search - Function
Glycosyl hydrolases family 9 (GH9) active site signature 1. / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / Endoglucanase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 Å
AuthorsMarcelo, M.V. / Campos, B.M. / Squina, F.M.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/04105-4 Brazil
Sao Paulo Research Foundation (FAPESP)2015/50590-4 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)310177/2011-1 Brazil
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions.
Authors: Liberato, M.V. / Campos, B.M. / Tomazetto, G. / Crouch, L.I. / Garcia, W. / Zeri, A.C.M. / Bolam, D.N. / Squina, F.M.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8244
Polymers16,6051
Non-polymers2193
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-3 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.739, 47.270, 79.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-927-

HOH

-
Components

#1: Protein Endoglucanase / Cellulase / Cellulase / Endo-1 / 4-beta-glucanase / Spore germination protein 270-6


Mass: 16605.338 Da / Num. of mol.: 1
Fragment: carbohydrate-binding module (UNP residues 555-705)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: celA, DDB_G0271134 / Production host: Escherichia coli (E. coli) / References: UniProt: P22699
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.6 M di-sodium DL-malate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45863 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45863 Å / Relative weight: 1
ReflectionResolution: 1.46→47.27 Å / Num. obs: 23773 / % possible obs: 96.9 % / Redundancy: 9 % / Biso Wilson estimate: 10.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.023 / Rrim(I) all: 0.076 / Net I/σ(I): 19.4 / Num. measured all: 215097 / Scaling rejects: 221
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.46-1.493.80.229398510490.9560.1310.2664.890.9
8.02-47.279.30.06217811920.9960.0220.06530.799.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.88 Å40.62 Å

-
Processing

Software
NameVersionClassification
iMOSFLM7.3.0data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7T7Y

7t7y


Resolution: 1.46→40.62 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 1113 4.69 %
Rwork0.1523 22619 -
obs0.154 23732 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.46 Å2 / Biso mean: 11.7208 Å2 / Biso min: 3.42 Å2
Refinement stepCycle: final / Resolution: 1.46→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 14 219 1385
Biso mean--11.49 22.93 -
Num. residues----154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.530.24761300.22499262987
1.53-1.610.2141220.16032742286496
1.61-1.710.16481550.15832769292496
1.71-1.840.22741510.16042733288495
1.84-2.030.17441270.140729033030100
2.03-2.320.21891410.146529083049100
2.32-2.930.20211400.153129623102100
2.93-40.620.16121470.147331033250100
Refinement TLS params.Method: refined / Origin x: 27.8695 Å / Origin y: 15.9389 Å / Origin z: 25.7389 Å
111213212223313233
T0.0426 Å2-0.0028 Å20.0011 Å2-0.038 Å2-0.0009 Å2--0.0235 Å2
L0.9228 °2-0.1096 °2-0.003 °2-0.9124 °20.2075 °2--0.3966 °2
S0.0025 Å °-0.0283 Å °0.0146 Å °0.0315 Å °0.0074 Å °-0.0421 Å °0 Å °0.0262 Å °-0.0066 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 552 through 705)

+
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