[English] 日本語
Yorodumi
- PDB-24tf: Crystal structure of GH30 endo-beta-1,6-galactanase from Streptom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 24tf
TitleCrystal structure of GH30 endo-beta-1,6-galactanase from Streptomyces avermitilis soaked with Gal-beta1,6-Gal-beta1,6-Gal.
ComponentsSecreted endo-beta-1,6-galactanase
KeywordsHYDROLASE / glycoside hydrolase family 30
Function / homologyEndo-beta-1,6-galactanase/Exo-beta-1,6-galactobiohydrolase / hydrolase activity, hydrolyzing O-glycosyl compounds / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycoside hydrolase superfamily / beta-D-galactopyranose / Secreted endo-beta-1,6-galactanase
Function and homology information
Biological speciesStreptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFujimoto, Z. / Kishine, N. / Kaneko, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Crystal structure of endo-beta-1,6-galactanase from Streptomyces avermitilis.
Authors: Fujimoto, Z. / Kishine, N. / Kotake, T. / Kaneko, S.
History
DepositionMar 19, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Secreted endo-beta-1,6-galactanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,67211
Polymers52,2941
Non-polymers1,37810
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-14 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.636, 50.636, 330.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-818-

HOH

21A-1122-

HOH

31A-1127-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Secreted endo-beta-1,6-galactanase


Mass: 52293.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
Gene: SAVERM_5205 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q82CY3

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 582 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density meas: 39.4 Mg/m3 / Density % sol: 39.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10% dioxane

-
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: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 48189 / % possible obs: 97.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.193 / Net I/σ(I): 16.1
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3203

-
Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.464 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.736 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 2416 5.029 %RANDOM
Rwork0.1486 45629 --
all0.15 ---
obs-48045 97.714 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 9.731 Å2
Baniso -1Baniso -2Baniso -3
1--0.048 Å2-0 Å20 Å2
2---0.048 Å2-0 Å2
3---0.097 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 85 574 4206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123733
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163317
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.7665103
X-RAY DIFFRACTIONr_angle_other_deg0.4731.7337599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2295465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.208522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.32310520
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.02410158
X-RAY DIFFRACTIONr_chiral_restr0.0620.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
X-RAY DIFFRACTIONr_nbd_refined0.20.2703
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.23137
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21863
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21822
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2430
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0890.216
X-RAY DIFFRACTIONr_nbd_other0.1620.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.274
X-RAY DIFFRACTIONr_mcbond_it0.4810.9831863
X-RAY DIFFRACTIONr_mcbond_other0.4770.9821863
X-RAY DIFFRACTIONr_mcangle_it0.8141.7642327
X-RAY DIFFRACTIONr_mcangle_other0.8141.7652328
X-RAY DIFFRACTIONr_scbond_it0.7121.1031870
X-RAY DIFFRACTIONr_scbond_other0.7121.1041871
X-RAY DIFFRACTIONr_scangle_it1.1531.9882776
X-RAY DIFFRACTIONr_scangle_other1.1531.9882777
X-RAY DIFFRACTIONr_lrange_it3.38713.8394524
X-RAY DIFFRACTIONr_lrange_other2.88810.5024325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.2651920.19333490.19735580.9580.97599.52220.193
1.744-1.7920.2071680.17332820.17534550.9720.9899.85530.173
1.792-1.8440.2271680.17431390.17633290.9660.97999.33910.174
1.844-1.9010.2271560.16230930.16532810.9680.98299.02470.162
1.901-1.9630.1781530.15429780.15531740.9760.98398.64520.154
1.963-2.0320.2051420.15129290.15331170.9720.98498.52420.151
2.032-2.1080.1881490.15528050.15730030.9730.98498.36830.155
2.108-2.1940.1711470.14626430.14728360.980.98698.3780.146
2.194-2.2910.1541310.13925740.13927660.9840.98797.79470.139
2.291-2.4030.1781200.13224640.13526670.980.98896.88790.132
2.403-2.5330.1621190.12923210.13125340.9810.98996.29050.129
2.533-2.6860.1611160.13221980.13423920.9830.98896.73910.132
2.686-2.8710.1551060.13420740.13522640.9830.98896.28980.134
2.871-3.10.1831040.14319330.14621260.9760.98695.81370.143
3.1-3.3940.174900.14517760.14619980.9820.98793.39340.145
3.394-3.7920.146960.13916180.13918010.9880.98995.16930.139
3.792-4.3750.145860.12314240.12416080.9870.9993.90550.123
4.375-5.3470.158730.14212910.14313960.9860.98997.70770.142
5.347-7.5160.25610.19910690.20211300.9710.9821000.199
7.516-48.4640.24390.2096690.2117130.9660.97599.29870.209

+
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