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- PDB-24tg: Crystal structure of selenomethionine labelled Streptomyces averm... -

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Basic information

Entry
Database: PDB / ID: 24tg
TitleCrystal structure of selenomethionine labelled Streptomyces avermitilis endo-beta-1,6-galactanase
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 / Secreted endo-beta-1,6-galactanase
Function and homology information
Biological speciesStreptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.001 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted endo-beta-1,6-galactanase
B: Secreted endo-beta-1,6-galactanase
C: Secreted endo-beta-1,6-galactanase
D: Secreted endo-beta-1,6-galactanase


Theoretical massNumber of molelcules
Total (without water)211,0514
Polymers211,0514
Non-polymers00
Water26,7881487
1
A: Secreted endo-beta-1,6-galactanase


Theoretical massNumber of molelcules
Total (without water)52,7631
Polymers52,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted endo-beta-1,6-galactanase


Theoretical massNumber of molelcules
Total (without water)52,7631
Polymers52,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Secreted endo-beta-1,6-galactanase


Theoretical massNumber of molelcules
Total (without water)52,7631
Polymers52,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Secreted endo-beta-1,6-galactanase


Theoretical massNumber of molelcules
Total (without water)52,7631
Polymers52,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.173, 233.013, 87.885
Angle α, β, γ (deg.)90.000, 94.855, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 52762.668 Da / Num. of mol.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1487 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.7 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 17% PEG4000, 20% isopropanol, 0.1 M Sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 114201 / % possible obs: 98.4 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 14.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 11437

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.001→43.769 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.944 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.168
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 5701 5.004 %RANDOM
Rwork0.1693 108230 --
all0.172 ---
obs-113931 98.269 %-
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: 14.035 Å2
Baniso -1Baniso -2Baniso -3
1--0.034 Å20 Å20.011 Å2
2--0.018 Å2-0 Å2
3---0.014 Å2
Refinement stepCycle: LAST / Resolution: 2.001→43.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14356 0 0 1487 15843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01214746
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.76320160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03551880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.735587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.104101979
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.21810638
X-RAY DIFFRACTIONr_chiral_restr0.0930.22205
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211872
X-RAY DIFFRACTIONr_nbd_refined0.1920.27294
X-RAY DIFFRACTIONr_nbtor_refined0.3040.29999
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.21510
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.238
X-RAY DIFFRACTIONr_mcbond_it0.8131.3157532
X-RAY DIFFRACTIONr_mcangle_it1.372.3579408
X-RAY DIFFRACTIONr_scbond_it1.0191.3527214
X-RAY DIFFRACTIONr_scangle_it1.6192.44810752
X-RAY DIFFRACTIONr_lrange_it3.56715.19323962
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
2.001-2.0530.2244020.1880000.18286170.9670.97997.50490.153
2.053-2.1090.244160.18277370.18582510.9640.97898.81230.156
2.109-2.170.214170.17276300.17481300.9720.98198.97910.147
2.17-2.2370.23850.16973590.1778330.9730.98298.86380.145
2.237-2.310.2353890.16871540.17276660.9650.98298.39550.144
2.31-2.3910.243690.16968880.17273910.9640.98298.1870.145
2.391-2.4810.213370.16665770.16970680.9710.98397.82120.144
2.481-2.5810.2563490.17963400.18368560.9570.9897.56420.155
2.581-2.6960.2273000.16661530.16866400.9680.98397.18370.145
2.696-2.8270.2132840.1757650.17262440.9720.98296.8770.15
2.827-2.9790.2193090.1754580.17259670.9720.98296.64820.153
2.979-3.1590.2292780.17652780.17956850.9670.98197.73090.161
3.159-3.3760.2262640.17549840.17753480.970.98298.13010.162
3.376-3.6440.1952360.1746610.17149470.9770.98398.98930.161
3.644-3.9890.1972320.15742890.15945450.9770.98699.47190.15
3.989-4.4560.1792230.14638970.14841330.9810.98799.68550.14
4.456-5.1360.1731690.13834940.13936670.9840.98999.89090.135
5.136-6.2690.2191610.18229560.18431180.980.98399.96790.174
6.269-8.7760.2411160.20322940.20524120.9720.98399.91710.2
8.776-43.7690.188650.21113120.2113830.9640.97599.56620.219

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