[English] 日本語
Yorodumi
- PDB-8wac: Crystal structure of a novel agarose-binding carbohydrate binding... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wac
TitleCrystal structure of a novel agarose-binding carbohydrate binding module of an agarase
ComponentsAgarase
KeywordsSUGAR BINDING PROTEIN / A novel agarose-binding carbohydrate binding module
Function / homologyPorphyranase catalytic subdomain 1 / Beta-porphyranase A, C-terminal / beta porphyranase A C-terminal / Porphyranase beta-sandwich domain 1 / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Glycoside hydrolase superfamily / Agarase
Function and homology information
Biological speciesWenyingzhuangia fucanilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMei, X.W. / Chang, Y.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U22A20542 China
CitationJournal: To Be Published
Title: Crystal structure of a novel agarose-binding carbohydrate binding module of an agarase
Authors: Mei, X.W. / Chang, Y.G.
History
DepositionSep 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Agarase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2782
Polymers14,2371
Non-polymers401
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Agarase
hetero molecules

A: Agarase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5554
Polymers28,4752
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area940 Å2
ΔGint-14 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.661, 48.651, 67.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-201-

CA

21A-467-

HOH

31A-478-

HOH

41A-492-

HOH

51A-545-

HOH

61A-550-

HOH

71A-561-

HOH

81A-573-

HOH

-
Components

#1: Protein Agarase


Mass: 14237.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Carbohydrate binding module
Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria)
Gene: AXE80_01580 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B1Y2R0
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium chloride dihydrate, 20% 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: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.5→48.65 Å / Num. obs: 19954 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Rrim(I) all: 0.064 / Χ2: 1.01 / Net I/σ(I): 17.6 / Num. measured all: 118708
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.306 / Num. measured all: 3627 / Num. unique obs: 975 / CC1/2: 0.918 / Rpim(I) all: 0.18 / Rrim(I) all: 0.356 / Χ2: 0.93 / Net I/σ(I) obs: 3.6

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.28 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 1992 10 %
Rwork0.1684 --
obs0.1721 19919 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 1 284 1212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.793
X-RAY DIFFRACTIONf_dihedral_angle_d6.538132
X-RAY DIFFRACTIONf_chiral_restr0.066156
X-RAY DIFFRACTIONf_plane_restr0.006180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.28481410.23291272X-RAY DIFFRACTION100
1.54-1.580.26871380.20531232X-RAY DIFFRACTION100
1.58-1.630.25041400.19631272X-RAY DIFFRACTION100
1.63-1.680.2471410.21381262X-RAY DIFFRACTION100
1.68-1.740.22921400.19431267X-RAY DIFFRACTION100
1.74-1.810.24321390.18651243X-RAY DIFFRACTION100
1.81-1.890.20891400.17411266X-RAY DIFFRACTION100
1.89-1.990.18281410.17121268X-RAY DIFFRACTION100
1.99-2.110.19961430.16841289X-RAY DIFFRACTION100
2.11-2.280.19431410.16131264X-RAY DIFFRACTION100
2.28-2.510.22951420.17781283X-RAY DIFFRACTION100
2.51-2.870.2011450.1741308X-RAY DIFFRACTION100
2.87-3.610.21091460.15261306X-RAY DIFFRACTION100
3.62-29.280.16291550.14281395X-RAY DIFFRACTION100

+
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