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- PDB-9p2e: Crystal structure of GH158(Pro) soaked with mixed linkage (G3G4G)... -

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Basic information

Entry
Database: PDB / ID: 9p2e
TitleCrystal structure of GH158(Pro) soaked with mixed linkage (G3G4G) oligosaccharide at 1.70 angstrom resolution
ComponentsGlycoside hydrolase family 158
KeywordsHYDROLASE / Enzyme / glycoside hydrolase / glucanase
Function / homologybeta-D-glucopyranose
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSpadeto, J.P.M. / Martins, M.P. / Araujo, E.A. / Mandelli, F. / Domingues, M.N. / Morais, M.A.B. / Murakami, M.T.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
Sao Paulo Research Foundation (FAPESP)2022/06298-0 Brazil
CitationJournal: To Be Published
Title: Crystal structure of GH158(Pro) soaked with mixed linkage (G3G4G) oligosaccharide at 1.70 angstrom resolution
Authors: Spadeto, J.P.M. / Martins, M.P. / Araujo, E.A. / Mandelli, F. / Domingues, M.N. / Morais, M.A.B. / Murakami, M.T.
History
DepositionJun 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0585
Polymers46,4651
Non-polymers5934
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.244, 70.857, 117.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoside hydrolase family 158


Mass: 46464.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: glucan endo-1,3-beta-D-glucosidase
#2: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


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
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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% PEG400, 18% PEG8000, 0.1M TRIS pH 8.5, 0.1M MgCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.7→48.24 Å / Num. obs: 45126 / % possible obs: 99.9 % / Redundancy: 12.65 % / CC1/2: 0.993 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.137 / Net I/σ(I): 4.85
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.7-1.81.10944580.2761.4021
1.8-1.930.62243400.5380.7991
1.93-2.080.33640380.8320.4211
2.08-2.280.21136170.9310.2611
2.28-2.550.16732360.950.2061
2.55-2.940.11327480.9770.1391
2.94-3.60.0722760.990.0871
3.6-5.070.04717440.9940.0561
5.07-48.240.0539260.9910.0641

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.21 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 2256 5 %
Rwork0.167 --
obs0.1686 45078 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 36 188 3345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083257
X-RAY DIFFRACTIONf_angle_d1.0844432
X-RAY DIFFRACTIONf_dihedral_angle_d14.7121211
X-RAY DIFFRACTIONf_chiral_restr0.064481
X-RAY DIFFRACTIONf_plane_restr0.026580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.40021380.36842594X-RAY DIFFRACTION98
1.74-1.780.33931390.2952643X-RAY DIFFRACTION100
1.78-1.820.33931390.26532632X-RAY DIFFRACTION100
1.82-1.870.30131390.22852652X-RAY DIFFRACTION100
1.87-1.930.2861390.21422637X-RAY DIFFRACTION100
1.93-1.990.21431390.19982643X-RAY DIFFRACTION100
1.99-2.060.25491390.19042643X-RAY DIFFRACTION100
2.06-2.140.19351410.17862680X-RAY DIFFRACTION100
2.14-2.240.17141400.15442648X-RAY DIFFRACTION100
2.24-2.360.20541400.15632659X-RAY DIFFRACTION100
2.36-2.50.17511410.16142679X-RAY DIFFRACTION100
2.5-2.70.2111410.16532685X-RAY DIFFRACTION100
2.7-2.970.18431420.16042698X-RAY DIFFRACTION100
2.97-3.40.17561420.15432699X-RAY DIFFRACTION100
3.4-4.280.15961450.13252752X-RAY DIFFRACTION100
4.28-45.210.1691520.14352878X-RAY DIFFRACTION100

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