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- PDB-9p2d: Crystal structure of GH158(Pro) at 1.30 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 9p2d
TitleCrystal structure of GH158(Pro) at 1.30 angstrom resolution
ComponentsGH158(Pro)
KeywordsHYDROLASE / Enzyme / glycoside hydrolase / glucanase
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSpadeto, J.P.M. / Martins, M.P. / Araujo, E.A. / Mandelli, F. / Domingues, M.N. / Santos, C.A. / Santos, C.R. / 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: Nat Commun / Year: 2026
Title: Conformational gating mechanism for processive catalysis of beta (1,3)-glucans.
Authors: Gimenis, G.H.B. / Spadeto, J.P.M. / Colombari, F.M. / Miyamoto, R.Y. / Higasi, P.M.R. / Santos, C.A. / Mandelli, F. / Martins, M.P. / Araujo, E.A. / Domingues, M.N. / Fuzita, F.J. / ...Authors: Gimenis, G.H.B. / Spadeto, J.P.M. / Colombari, F.M. / Miyamoto, R.Y. / Higasi, P.M.R. / Santos, C.A. / Mandelli, F. / Martins, M.P. / Araujo, E.A. / Domingues, M.N. / Fuzita, F.J. / Oliveira, A.M. / Gazolla, M.C. / Santos, C.R. / Persinoti, G.F. / Brumer, H. / Rovira, C. / Ramos, C.H.I. / 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
Revision 1.1Sep 30, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH158(Pro)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7805
Polymers46,4651
Non-polymers3154
Water11,133618
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)48.108, 70.557, 115.538
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)


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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O
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: 41.71 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.86214 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86214 Å / Relative weight: 1
ReflectionResolution: 1.3→48.11 Å / Num. obs: 97429 / % possible obs: 100 % / Redundancy: 13.34 % / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.155 / Net I/σ(I): 3.97
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.3-1.381.591106600.132.0351
1.38-1.471.2199610.211.5371
1.47-1.590.80390770.4291.0131
1.59-1.740.52881840.6480.6641
1.74-1.950.29271580.8740.3651
1.95-2.250.14559600.9720.1781
2.25-2.750.09346680.9860.1121
2.75-3.890.05437030.9950.0641
3.89-48.110.04119570.9970.0481

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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: 1.3→44.7 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 4865 5 %
Rwork0.1594 --
obs0.1611 97363 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 18 616 3771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113271
X-RAY DIFFRACTIONf_angle_d1.234451
X-RAY DIFFRACTIONf_dihedral_angle_d12.7921224
X-RAY DIFFRACTIONf_chiral_restr0.098470
X-RAY DIFFRACTIONf_plane_restr0.013588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.34531520.31552971X-RAY DIFFRACTION97
1.31-1.330.32761620.27273075X-RAY DIFFRACTION100
1.33-1.350.28461580.25643005X-RAY DIFFRACTION100
1.35-1.360.3511600.25743037X-RAY DIFFRACTION100
1.36-1.380.2791630.24593095X-RAY DIFFRACTION100
1.38-1.40.311590.23713012X-RAY DIFFRACTION100
1.4-1.420.27751620.22333093X-RAY DIFFRACTION100
1.42-1.440.27571600.21173026X-RAY DIFFRACTION100
1.44-1.460.26091610.20663068X-RAY DIFFRACTION100
1.46-1.490.24951600.19523029X-RAY DIFFRACTION100
1.49-1.510.26971610.18583060X-RAY DIFFRACTION100
1.51-1.540.23321620.17343075X-RAY DIFFRACTION100
1.54-1.570.23311600.17073056X-RAY DIFFRACTION100
1.57-1.60.20041630.16513080X-RAY DIFFRACTION100
1.6-1.640.21811600.16363047X-RAY DIFFRACTION100
1.64-1.680.22031630.16883095X-RAY DIFFRACTION100
1.68-1.720.19851600.15993053X-RAY DIFFRACTION100
1.72-1.760.21261620.15123064X-RAY DIFFRACTION100
1.76-1.820.16741620.14873082X-RAY DIFFRACTION100
1.82-1.870.19551610.14263066X-RAY DIFFRACTION100
1.87-1.940.19631640.14493109X-RAY DIFFRACTION100
1.94-2.020.19151630.15253091X-RAY DIFFRACTION100
2.02-2.110.1971610.14273066X-RAY DIFFRACTION100
2.11-2.220.16791630.14143103X-RAY DIFFRACTION100
2.22-2.360.16421650.14283120X-RAY DIFFRACTION100
2.36-2.540.15521630.14693112X-RAY DIFFRACTION100
2.54-2.80.20921650.16033124X-RAY DIFFRACTION100
2.8-3.210.18211670.15593170X-RAY DIFFRACTION100
3.21-4.040.16081670.13623183X-RAY DIFFRACTION100
4.04-44.70.15331760.14423331X-RAY DIFFRACTION100

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