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- PDB-9j6n: beta-D-galactofuranosidase ORF1110 from Streptomyces sp. JHA19, D... -

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Basic information

Entry
Database: PDB / ID: 9j6n
Titlebeta-D-galactofuranosidase ORF1110 from Streptomyces sp. JHA19, D-iminogalactitol complex
ComponentsBeta-D-galactofuranosidase 2
KeywordsHYDROLASE / Glycoside Hydrolase Family 2
Function / homology
Function and homology information


L-arabinose metabolic process / alpha-L-arabinofuranosidase activity
Similarity search - Function
Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / : / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 ...Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / : / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Beta-D-galactofuranosidase 2
Similarity search - Component
Biological speciesStreptomyces sp. JHA19 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsFujio, N. / Yamada, C. / Takegawa, K. / Fushinobu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Febs Lett. / Year: 2024
Title: Crystal structure of beta-d-galactofuranosidase from Streptomyces sp. JHA19 in complex with an inhibitor provides insights into substrate specificity.
Authors: Fujio, N. / Yamada, C. / Kashima, T. / Matsunaga, E. / Nash, R.J. / Takegawa, K. / Fushinobu, S.
#1: Journal: PLoS One / Year: 2015
Title: Identification and Characterization of a Novel Galactofuranose-Specific beta-D-Galactofuranosidase from Streptomyces Species.
Authors: Matsunaga, E. / Higuchi, Y. / Mori, K. / Yairo, N. / Oka, T. / Shinozuka, S. / Tashiro, K. / Izumi, M. / Kuhara, S. / Takegawa, K.
#2: Journal: Carbohydr Res / Year: 2019
Title: Galactofuranosidase from JHA 19 Streptomyces sp.: subcloning and biochemical characterization.
Authors: Senicar, M. / Legentil, L. / Ferrieres, V. / Eliseeva, S.V. / Petoud, S. / Takegawa, K. / Lafite, P. / Daniellou, R.
History
DepositionAug 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-D-galactofuranosidase 2
B: Beta-D-galactofuranosidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,34711
Polymers134,1412
Non-polymers1,2069
Water14,358797
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A: Beta-D-galactofuranosidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7776
Polymers67,0711
Non-polymers7065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-12 kcal/mol
Surface area19340 Å2
MethodPISA
2
B: Beta-D-galactofuranosidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5715
Polymers67,0711
Non-polymers5004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.364, 57.346, 109.732
Angle α, β, γ (deg.)90.00, 94.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-D-galactofuranosidase 2


Mass: 67070.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. JHA19 (bacteria) / Plasmid: pET50b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL-X / References: UniProt: A0A0K2SRV3

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Non-polymers , 6 types, 806 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-A1L3Z / (2~{S},3~{S},4~{S})-2-[(1~{S})-1,2-bis(oxidanyl)ethyl]pyrrolidine-3,4-diol


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 75mM potassium thiocyanate (KSCN), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2022
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.46 Å / Num. obs: 110248 / % possible obs: 98.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.55 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.061 / Net I/σ(I): 9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5375 / CC1/2: 0.658 / Rpim(I) all: 0.409 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→47.46 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.236 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18934 5434 4.9 %RANDOM
Rwork0.15332 ---
obs0.15508 104798 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.337 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å20.01 Å2
2--0.29 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.7→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8989 0 80 797 9866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129342
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168601
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.80812782
X-RAY DIFFRACTIONr_angle_other_deg0.5951.75719722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20551160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.608581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.618101350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022276
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4391.5194631
X-RAY DIFFRACTIONr_mcbond_other1.4291.5194630
X-RAY DIFFRACTIONr_mcangle_it2.0572.7245782
X-RAY DIFFRACTIONr_mcangle_other2.0572.7255783
X-RAY DIFFRACTIONr_scbond_it1.8561.6614711
X-RAY DIFFRACTIONr_scbond_other1.8561.6614712
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.822.9826997
X-RAY DIFFRACTIONr_long_range_B_refined4.17516.0110486
X-RAY DIFFRACTIONr_long_range_B_other4.02515.210311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 369 -
Rwork0.236 7687 -
obs--96.66 %

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