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- PDB-9p25: Crystal structure of GH158(Pro) at 0.89 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 9p25
TitleCrystal structure of GH158(Pro) at 0.89 angstrom resolution
ComponentsGH158(Pro)
KeywordsHYDROLASE / Enzyme / glycoside hydrolase / glucanase
Function / homology2-(2-ETHOXYETHOXY)ETHANOL / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 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 ProGH158 at 0.89 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: GH158(Pro)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0607
Polymers46,4651
Non-polymers5966
Water10,160564
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)48.280, 70.430, 115.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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) / References: glucan endo-1,3-beta-D-glucosidase

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Non-polymers , 6 types, 570 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#6: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.11 Å3/Da / Density % sol: 41.59 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.7872 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7872 Å / Relative weight: 1
ReflectionResolution: 0.89→44.56 Å / Num. obs: 293185 / % possible obs: 100 % / Redundancy: 24.01 % / CC1/2: 1 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.12 / Net I/σ(I): 24.92
Reflection shellResolution: 0.89→0.94 Å / Num. unique obs: 89314 / CC1/2: 0.166

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.89→44.56 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1532 2000 0.68 %
Rwork0.1455 --
obs0.1456 292933 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.89→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 37 564 3732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113271
X-RAY DIFFRACTIONf_angle_d1.2944439
X-RAY DIFFRACTIONf_dihedral_angle_d12.3421231
X-RAY DIFFRACTIONf_chiral_restr0.097468
X-RAY DIFFRACTIONf_plane_restr0.018584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.89-0.910.3971180.358717048X-RAY DIFFRACTION81
0.91-0.940.29591330.291519434X-RAY DIFFRACTION93
0.94-0.970.26471440.238121023X-RAY DIFFRACTION100
0.97-10.2271440.197920949X-RAY DIFFRACTION100
1-1.030.1741450.163521082X-RAY DIFFRACTION100
1.03-1.070.17241450.139121036X-RAY DIFFRACTION100
1.07-1.120.13681440.118321064X-RAY DIFFRACTION100
1.12-1.180.12941460.113221057X-RAY DIFFRACTION100
1.18-1.260.12551440.116721129X-RAY DIFFRACTION100
1.26-1.350.14161470.123721196X-RAY DIFFRACTION100
1.35-1.490.14181450.125221198X-RAY DIFFRACTION100
1.49-1.70.14681470.131121283X-RAY DIFFRACTION100
1.7-2.150.12731470.14621431X-RAY DIFFRACTION100
2.15-44.560.15691510.148622003X-RAY DIFFRACTION100

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