[English] 日本語
Yorodumi
- PDB-7b5v: The carbohydrate binding module family 48 (CBM48) and carboxy-ter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b5v
TitleThe carbohydrate binding module family 48 (CBM48) and carboxy-terminal carbohydrate esterase family 1 (CE1) domains of the multidomain esterase DmCE1B from Dysgonomonas mossii
ComponentsCarbohydrate Esterase family 1 protein with an N-terminal carbohydrate binding module family 48
KeywordsHYDROLASE / carbohydrate esterase / CE1 / CBM48 / carbohydrate binding module / CBM / CE / PUL / lignin / xylan / ferulate / ferouyl esterase
Function / homology: / Esterase-like / Putative esterase / acyltransferase activity, transferring groups other than amino-acyl groups / Immunoglobulin E-set / Alpha/Beta hydrolase fold / Immunoglobulin-like fold / DI(HYDROXYETHYL)ETHER / Esterase
Function and homology information
Biological speciesDysgonomonas mossii DSM 22836 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMazurkewich, S. / Kmezik, C. / Branden, G. / Larsbrink, J.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-03931 Sweden
Novo Nordisk FoundationNNF17OC0027648 Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases.
Authors: Kmezik, C. / Mazurkewich, S. / Meents, T. / McKee, L.S. / Idstrom, A. / Armeni, M. / Savolainen, O. / Branden, G. / Larsbrink, J.
History
DepositionDec 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 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: Carbohydrate Esterase family 1 protein with an N-terminal carbohydrate binding module family 48
B: Carbohydrate Esterase family 1 protein with an N-terminal carbohydrate binding module family 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9255
Polymers86,7212
Non-polymers2043
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-18 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.962, 80.966, 107.350
Angle α, β, γ (deg.)90.000, 105.666, 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 on special symmetry positions
IDModelComponents
11B-809-

HOH

-
Components

#1: Protein Carbohydrate Esterase family 1 protein with an N-terminal carbohydrate binding module family 48


Mass: 43360.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dysgonomonas mossii DSM 22836 (bacteria)
Gene: HMPREF9456_02279 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8X1N1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: JCSG - B9 - 0.1 M Citrate pH 5, 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.697→42.08 Å / Num. obs: 94462 / % possible obs: 99.63 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.15 Å2 / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 9.34
Reflection shellResolution: 1.697→1.757 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 9133 / CC1/2: 0.588 / CC star: 0.861 / % possible all: 96.87

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NE9

6ne9


Resolution: 1.7→42.08 Å / SU ML: 0.2239 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2683
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 7079 7.5 %
Rwork0.1684 87312 -
obs0.1716 94391 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5531 0 12 648 6191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735777
X-RAY DIFFRACTIONf_angle_d0.87457827
X-RAY DIFFRACTIONf_chiral_restr0.0612814
X-RAY DIFFRACTIONf_plane_restr0.00531030
X-RAY DIFFRACTIONf_dihedral_angle_d20.04012118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.41792030.40082528X-RAY DIFFRACTION87.36
1.72-1.740.37032390.32592944X-RAY DIFFRACTION99.94
1.74-1.760.29822320.31282858X-RAY DIFFRACTION99.94
1.76-1.780.33352370.29382919X-RAY DIFFRACTION100
1.78-1.80.29982360.28192917X-RAY DIFFRACTION100
1.8-1.830.29532380.26092930X-RAY DIFFRACTION99.97
1.83-1.850.2672340.24812887X-RAY DIFFRACTION99.97
1.85-1.880.26562380.23742939X-RAY DIFFRACTION99.97
1.88-1.910.29432320.23382863X-RAY DIFFRACTION100
1.91-1.940.28672390.24052959X-RAY DIFFRACTION99.91
1.94-1.970.24582340.21562874X-RAY DIFFRACTION99.97
1.97-2.010.22982370.19682918X-RAY DIFFRACTION99.94
2.01-2.050.23222370.18452931X-RAY DIFFRACTION99.97
2.05-2.090.21012350.17842900X-RAY DIFFRACTION100
2.09-2.140.23272370.17872932X-RAY DIFFRACTION100
2.14-2.190.22092380.17472918X-RAY DIFFRACTION99.84
2.19-2.240.22282370.17932922X-RAY DIFFRACTION100
2.24-2.30.20942330.18052884X-RAY DIFFRACTION100
2.3-2.370.23042420.17582973X-RAY DIFFRACTION99.97
2.37-2.450.21552360.1792918X-RAY DIFFRACTION99.9
2.45-2.530.21042360.18392901X-RAY DIFFRACTION99.9
2.53-2.630.21952400.18932956X-RAY DIFFRACTION99.94
2.63-2.750.222360.18472908X-RAY DIFFRACTION99.94
2.75-2.90.23362350.18332916X-RAY DIFFRACTION100
2.9-3.080.22082380.1812922X-RAY DIFFRACTION99.94
3.08-3.320.2022380.16782938X-RAY DIFFRACTION99.97
3.32-3.650.21122410.1512968X-RAY DIFFRACTION99.97
3.65-4.180.14162360.12862918X-RAY DIFFRACTION99.97
4.18-5.270.16112410.10482967X-RAY DIFFRACTION100
5.27-42.080.2042440.13673004X-RAY DIFFRACTION99.48

+
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