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- PDB-9g5g: Glycoside Hydrolase Family 157 from Labilibaculum antarcticum (La... -

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Basic information

Entry
Database: PDB / ID: 9g5g
TitleGlycoside Hydrolase Family 157 from Labilibaculum antarcticum (LaGH157) in complex with Laminaribiose
ComponentsGlycoside hydrolase family 2 catalytic domain-containing protein
KeywordsHYDROLASE / Glycoside hydrolase / endo-beta-1 / 3-glucanase / cazyme / ligand complex
Function / homologyGlycoside hydrolase superfamily / beta-laminaribiose / beta-D-glucopyranose / MALONIC ACID / Glycoside hydrolase family 2 catalytic domain-containing protein
Function and homology information
Biological speciesLabilibaculum antarcticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsCaseiro, C. / Alves, V.D. / Carvalho, A.L. / Bule, P.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)SFRH/BD/147152/2019, UIDB/00276/2020, LA/P/0059/2020 Portugal
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Family GH157 enzyme exhibits broad linkage tolerance and a dual endo/exo-beta-glucanase activity on beta-glucans.
Authors: Caseiro, C. / McGregor, N.G.S. / Alves, V.D. / Carvalho, A.L. / Romao, M.J. / Davies, G.J. / Fontes, C.M.G.A. / Bule, P.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 2 catalytic domain-containing protein
B: Glycoside hydrolase family 2 catalytic domain-containing protein
C: Glycoside hydrolase family 2 catalytic domain-containing protein
D: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,08017
Polymers246,0564
Non-polymers2,02413
Water3,405189
1
A: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2496
Polymers61,5141
Non-polymers7355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7863
Polymers61,5141
Non-polymers2722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9044
Polymers61,5141
Non-polymers3903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1414
Polymers61,5141
Non-polymers6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.628, 208.628, 165.285
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycoside hydrolase family 2 catalytic domain-containing protein


Mass: 61514.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Labilibaculum antarcticum (bacteria) / Gene: ALGA_4297 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1CQ89

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 198 molecules

#3: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium malonate, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.71→121.95 Å / Num. obs: 71618 / % possible obs: 98.6 % / Redundancy: 6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.074 / Rrim(I) all: 0.182 / Χ2: 0.99 / Net I/σ(I): 9.6 / Num. measured all: 429854
Reflection shellResolution: 2.71→2.77 Å / % possible obs: 83.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 1.894 / Num. measured all: 21966 / Num. unique obs: 3895 / CC1/2: 0.375 / Rpim(I) all: 0.86 / Rrim(I) all: 2.086 / Χ2: 0.71 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→121.95 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / SU B: 52.537 / SU ML: 0.46 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 3618 5.1 %RANDOM
Rwork0.21083 ---
obs0.21388 68000 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.207 Å2
Baniso -1Baniso -2Baniso -3
1-4.19 Å22.1 Å2-0 Å2
2--4.19 Å2-0 Å2
3----13.6 Å2
Refinement stepCycle: 1 / Resolution: 2.71→121.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17000 0 135 189 17324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01217522
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616232
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.8223681
X-RAY DIFFRACTIONr_angle_other_deg0.5521.77837666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03152108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.511544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.613103116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.22536
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0220200
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023832
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_it1.0541.4998444
X-RAY DIFFRACTIONr_mcbond_other1.0541.4998444
X-RAY DIFFRACTIONr_mcangle_it1.7692.69110548
X-RAY DIFFRACTIONr_mcangle_other1.7692.69210549
X-RAY DIFFRACTIONr_scbond_it1.4391.6499078
X-RAY DIFFRACTIONr_scbond_other1.4381.6489077
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2042.97913134
X-RAY DIFFRACTIONr_long_range_B_refined7.49214.4819649
X-RAY DIFFRACTIONr_long_range_B_other7.49114.4619639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.712→2.783 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 237 -
Rwork0.355 4357 -
obs--85.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0970.08990.04962.21420.44840.81-0.04520.1362-0.0520.0840.0903-0.26660.20590.1065-0.04510.05790.01710.05130.0667-0.02541.622744.132-19.077-2.104
20.73540.11720.12531.90930.39291.056-0.06960.00370.07350.26820.0709-0.1329-0.0728-0.0543-0.00120.06180.0184-0.03980.00760.00171.666733.06418.16512.682
32.783-0.29420.50050.7587-0.07082.2949-0.0665-0.14370.35820.14180.02240.0841-0.465-0.53530.04420.23660.22930.13340.3082-0.02941.814141.86541.002-48.259
43.4173-0.21790.25411.3021-0.31031.3452-0.0591-0.88340.47350.2716-0.0615-0.1667-0.19620.25330.12060.25410.08730.03570.4949-0.0481.780178.88130.152-32.889
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D3 - 530
2X-RAY DIFFRACTION2A3 - 530
3X-RAY DIFFRACTION3B3 - 530
4X-RAY DIFFRACTION4C3 - 530

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