[English] 日本語
Yorodumi
- PDB-7byx: Crystal structure of exo-beta-1,3-galactanase from Phanerochaete ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7byx
TitleCrystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A E208A with beta-1,3-galactotriose
ComponentsGalactan 1,3-beta-galactosidase
KeywordsHYDROLASE / Glycoside hydrolase family 43 / exo-beta-1 / 3-galactanase / arabinogalactan degrade / complex with beta-1 / 3-galactotriose / carbohydrate binding module family 35
Function / homology
Function and homology information


galactan 1,3-beta-galactosidase / galactan 1,3-beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Galactan 1,3-beta-galactosidase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMatsuyama, K. / Ishida, T. / Kishine, N. / Fujimoto, Z. / Igarashi, K. / Kaneko, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05494 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-beta-1,3-galactanase from Phanerochaete chrysosporium .
Authors: Matsuyama, K. / Kishine, N. / Fujimoto, Z. / Sunagawa, N. / Kotake, T. / Tsumuraya, Y. / Samejima, M. / Igarashi, K. / Kaneko, S.
History
DepositionApr 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galactan 1,3-beta-galactosidase
B: Galactan 1,3-beta-galactosidase
C: Galactan 1,3-beta-galactosidase
D: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,23252
Polymers181,9104
Non-polymers10,32248
Water18,1231006
1
A: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,72917
Polymers45,4781
Non-polymers3,25116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,76010
Polymers45,4781
Non-polymers2,2829
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,94412
Polymers45,4781
Non-polymers2,46611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,80013
Polymers45,4781
Non-polymers2,32212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.737, 156.737, 147.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
D: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-940-

HOH

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Galactan 1,3-beta-galactosidase / exo-beta-1 / 3-galactanase


Mass: 45477.613 Da / Num. of mol.: 4 / Mutation: E208A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: Pc1,3Gal43A / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H
References: UniProt: Q50KB2, galactan 1,3-beta-galactosidase

-
Sugars , 6 types, 16 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2112h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-Galp]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#10: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 1038 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 % / Description: bipyramidial
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M potassium nitrate, 15 % (w/v) polyethylene glycol 6000, 20 mM sodium citrate, 5 % glycerol, 10 mM beta-1,3-galactotriose

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 92497 / % possible obs: 99.1 % / Redundancy: 9.7 % / Biso Wilson estimate: 30.4 Å2 / Rsym value: 0.167 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8510 / Rsym value: 0.627 / % possible all: 92

-
Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
REFMAC5.8.0158refinement
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BYS

7bys


Resolution: 2.3→31.14 Å / SU ML: 0.2633 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 4569 4.97 %Random selection
Rwork0.161 87425 --
obs0.1637 91994 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12856 0 678 1006 14540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007613873
X-RAY DIFFRACTIONf_angle_d0.951518897
X-RAY DIFFRACTIONf_chiral_restr0.06322116
X-RAY DIFFRACTIONf_plane_restr0.00532416
X-RAY DIFFRACTIONf_dihedral_angle_d4.37619641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.31361330.23332531X-RAY DIFFRACTION87
2.33-2.350.28061720.2222664X-RAY DIFFRACTION91.99
2.35-2.380.25691360.2182871X-RAY DIFFRACTION97.47
2.38-2.410.27051620.21332871X-RAY DIFFRACTION99.09
2.41-2.440.32821650.2112909X-RAY DIFFRACTION99.19
2.44-2.480.26741540.20792904X-RAY DIFFRACTION99.41
2.48-2.510.28961560.19962895X-RAY DIFFRACTION99.16
2.51-2.550.27891410.20082892X-RAY DIFFRACTION99.21
2.55-2.590.30261360.19992911X-RAY DIFFRACTION99.19
2.59-2.630.23811690.18742874X-RAY DIFFRACTION99.19
2.63-2.680.26321600.18312917X-RAY DIFFRACTION99.64
2.68-2.730.24881540.18512913X-RAY DIFFRACTION99.22
2.73-2.780.26591370.18872902X-RAY DIFFRACTION99.31
2.78-2.840.2441120.18392990X-RAY DIFFRACTION99.52
2.84-2.90.2261520.18172896X-RAY DIFFRACTION99.25
2.9-2.960.25051560.16882881X-RAY DIFFRACTION99.15
2.96-3.040.22691390.17152969X-RAY DIFFRACTION99.65
3.04-3.120.22231830.16052923X-RAY DIFFRACTION99.74
3.12-3.210.19491450.15462925X-RAY DIFFRACTION99.55
3.21-3.320.21571750.15812911X-RAY DIFFRACTION99.87
3.32-3.430.23571300.15492978X-RAY DIFFRACTION99.94
3.43-3.570.1981450.14292944X-RAY DIFFRACTION99.9
3.57-3.730.17971790.13842921X-RAY DIFFRACTION99.97
3.73-3.930.18751370.1392981X-RAY DIFFRACTION99.97
3.93-4.180.19911610.1362967X-RAY DIFFRACTION100
4.18-4.50.15151290.12322991X-RAY DIFFRACTION99.94
4.5-4.950.1461840.11492949X-RAY DIFFRACTION99.9
4.95-5.660.18111500.13483003X-RAY DIFFRACTION99.9
5.66-7.120.21440.1613038X-RAY DIFFRACTION100
7.12-31.140.20471730.18523104X-RAY DIFFRACTION99.45

+
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://pdbjlvh1.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