[English] 日本語
Yorodumi
- PDB-8j3x: Crystal structure of CBM6E from Saccharophagus degradans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8j3x
TitleCrystal structure of CBM6E from Saccharophagus degradans
ComponentsPutative polysaccharide-binding protein
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


fungal-type cell wall polysaccharide metabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
: / Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Putative polysaccharide-binding protein
Similarity search - Component
Biological speciesSaccharophagus degradans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsHe, C. / Li, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biotechnol Biofuels Bioprod / Year: 2024
Title: Structural insights into curdlan degradation via a glycoside hydrolase containing a disruptive carbohydrate-binding module.
Authors: Lv, T. / Feng, J. / Jia, X. / Wang, C. / Li, F. / Peng, H. / Xiao, Y. / Liu, L. / He, C.
History
DepositionApr 18, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative polysaccharide-binding protein
B: Putative polysaccharide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1895
Polymers90,0482
Non-polymers1413
Water3,135174
1
A: Putative polysaccharide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1403
Polymers45,0241
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint2 kcal/mol
Surface area15560 Å2
MethodPISA
2
B: Putative polysaccharide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0482
Polymers45,0241
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.807, 146.033, 76.847
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Putative polysaccharide-binding protein


Mass: 45023.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024) (bacteria)
Gene: cbm6E, Sde_1445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21KS2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M bis-tris, pH 5.5, 25% (w/v) polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.4→19.68 Å / Num. obs: 37821 / % possible obs: 99.5 % / Redundancy: 8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.054 / Rrim(I) all: 0.156 / Χ2: 1 / Net I/σ(I): 10.7 / Num. measured all: 301592
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 99.2 % / Redundancy: 8.3 % / Rmerge(I) obs: 1.003 / Num. measured all: 32511 / Num. unique obs: 3916 / CC1/2: 0.811 / Rpim(I) all: 0.362 / Rrim(I) all: 1.068 / Χ2: 0.97 / Net I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.68 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1836 4.86 %
Rwork0.1824 --
obs0.1848 37767 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6257 0 8 174 6439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086450
X-RAY DIFFRACTIONf_angle_d0.928798
X-RAY DIFFRACTIONf_dihedral_angle_d14.1842253
X-RAY DIFFRACTIONf_chiral_restr0.053899
X-RAY DIFFRACTIONf_plane_restr0.0081151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.3361380.27012698X-RAY DIFFRACTION99
2.46-2.540.30851410.25192710X-RAY DIFFRACTION99
2.54-2.620.3041220.24212746X-RAY DIFFRACTION99
2.62-2.710.28021380.22952704X-RAY DIFFRACTION99
2.71-2.820.30911580.23162728X-RAY DIFFRACTION99
2.82-2.950.2861400.2332734X-RAY DIFFRACTION99
2.95-3.10.25711390.20992740X-RAY DIFFRACTION100
3.1-3.30.25681360.20422750X-RAY DIFFRACTION99
3.3-3.550.2291430.17572758X-RAY DIFFRACTION100
3.55-3.90.20361300.16262790X-RAY DIFFRACTION100
3.9-4.460.20441430.13842810X-RAY DIFFRACTION100
4.46-5.60.16761360.14252841X-RAY DIFFRACTION100
5.6-19.680.21471720.17522922X-RAY DIFFRACTION100
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)
10.68430.1796-0.23665.1594-0.6161.8653-0.06920.14730.0399-0.8589-0.096-0.66810.07870.0570.09820.36710.01810.06610.42110.04660.5169-19.248110.7675-45.5949
21.49-0.34610.58683.1736-0.70792.4262-0.1202-0.2360.20641.0292-0.0091-0.4216-0.3582-0.0050.14060.5506-0.0182-0.18670.356-0.03690.4275-22.566320.2801-15.9377
30.89740.80740.75632.6498-0.84572.11670.0649-0.1349-0.31291.2251-0.2552-0.89170.25010.4032-0.13230.89360.0168-0.30510.55020.14810.7213-14.6528-19.3931-5.0066
42.04330.7908-0.04983.601-0.34892.74560.0319-0.2691-0.03940.9804-0.1919-0.0588-0.2515-0.04870.12510.57650.0325-0.04220.40040.02480.3565-26.43-8.9494-10.1719
50.87340.2701-0.07973.04080.00062.0563-0.03950.085-0.1855-0.18290.0289-0.1960.1574-0.03640.01630.20630.02680.04030.3243-0.00390.425-25.6806-22.7877-37.3084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 85 through 319 )
2X-RAY DIFFRACTION2chain 'A' and (resid 320 through 473 )
3X-RAY DIFFRACTION3chain 'B' and (resid 84 through 196 )
4X-RAY DIFFRACTION4chain 'B' and (resid 197 through 319 )
5X-RAY DIFFRACTION5chain 'B' and (resid 320 through 473 )

+
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