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- PDB-9p28: Crystal structure of GH158(Pro) soaked with laminaritriose at 1.3... -

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Basic information

Entry
Database: PDB / ID: 9p28
TitleCrystal structure of GH158(Pro) soaked with laminaritriose at 1.30 angstrom resolution.
ComponentsGH158(Pro)
KeywordsHYDROLASE / Enzyme / glycoside hydrolase / glucanase
Function / homologybeta-laminaribiose / beta-D-glucopyranose
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMartins, M.P. / Spadeto, J.P.M. / 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 ProGH158 soaked with laminaritriose at 1.30 angstrom resolution.
Authors: Martins, M.P. / Spadeto, J.P.M. / 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: GH158(Pro)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0585
Polymers46,4651
Non-polymers5934
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.388, 71.113, 117.704
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 GH158(Pro) / 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)
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 1
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
#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.: 223 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: : 20% PEG3350, 25% PEG400, 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: Aug 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.3→48.39 Å / Num. obs: 100526 / % possible obs: 100 % / Redundancy: 12.905 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.061 / Net I/σ(I): 7.05
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.3-1.381.012110270.2591.3481
1.38-1.470.657104690.4890.8691
1.47-1.590.3796050.770.4851
1.59-1.740.21985240.9110.2851
1.74-1.950.11674620.9740.1491
1.95-2.250.06763930.9910.0841
2.25-2.750.04851170.9950.061
2.75-3.890.0337410.9980.0371

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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: 1.3→45.34 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1626 5027 5 %
Rwork0.1433 --
obs0.1442 100493 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 37 223 3381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093274
X-RAY DIFFRACTIONf_angle_d1.1484460
X-RAY DIFFRACTIONf_dihedral_angle_d12.8341212
X-RAY DIFFRACTIONf_chiral_restr0.09484
X-RAY DIFFRACTIONf_plane_restr0.023585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.42231650.37943102X-RAY DIFFRACTION99
1.31-1.330.33931640.33133108X-RAY DIFFRACTION100
1.33-1.350.33391670.28833189X-RAY DIFFRACTION100
1.35-1.360.30311660.26253145X-RAY DIFFRACTION100
1.36-1.380.26161660.24343152X-RAY DIFFRACTION100
1.38-1.40.25861640.21773127X-RAY DIFFRACTION100
1.4-1.420.23971670.20043171X-RAY DIFFRACTION100
1.42-1.440.24061640.18183118X-RAY DIFFRACTION100
1.44-1.460.22251680.16313189X-RAY DIFFRACTION100
1.46-1.490.20841650.15063133X-RAY DIFFRACTION100
1.49-1.510.181670.14483172X-RAY DIFFRACTION100
1.51-1.540.16821650.14633136X-RAY DIFFRACTION100
1.54-1.570.17411660.14823150X-RAY DIFFRACTION100
1.57-1.60.1761670.14993174X-RAY DIFFRACTION100
1.6-1.640.17751670.14933171X-RAY DIFFRACTION100
1.64-1.680.17971660.14323150X-RAY DIFFRACTION100
1.68-1.720.17031680.1333185X-RAY DIFFRACTION100
1.72-1.760.16681650.12643152X-RAY DIFFRACTION100
1.76-1.820.14261670.11543175X-RAY DIFFRACTION100
1.82-1.870.151680.10063182X-RAY DIFFRACTION100
1.87-1.940.1321670.10523181X-RAY DIFFRACTION100
1.94-2.020.12881680.11063189X-RAY DIFFRACTION100
2.02-2.110.13471680.11623183X-RAY DIFFRACTION100
2.11-2.220.1191680.10743206X-RAY DIFFRACTION100
2.22-2.360.12761690.11743200X-RAY DIFFRACTION100
2.36-2.540.15141710.13023248X-RAY DIFFRACTION100
2.54-2.80.16221680.14393201X-RAY DIFFRACTION100
2.8-3.210.15451710.14543245X-RAY DIFFRACTION100
3.21-4.040.15151740.13633297X-RAY DIFFRACTION100
4.04-45.340.17121810.16373435X-RAY DIFFRACTION100

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