[English] 日本語
Yorodumi
- PDB-9p2a: Crystal structure of GH158(Pro) soaked with laminaripentaose at 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9p2a
TitleCrystal structure of GH158(Pro) soaked with laminaripentaose at 1.45 angstrom resolution
ComponentsGH158(Pro)
KeywordsHYDROLASE / Enzyme / glycoside hydrolase / glucanase
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GH158(Pro)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2205
Polymers46,4651
Non-polymers7564
Water4,071226
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)48.291, 70.938, 117.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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) / 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.: 2
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
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#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.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% PEG400, 22% PEG8000, 0.1M TRIS pH 8.5, 0.1M MgCl2

-
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: 1.45→48.29 Å / Num. obs: 72685 / % possible obs: 77.8 % / Redundancy: 13.12 % / CC1/2: 0.988 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.176 / Net I/σ(I): 2.74
Reflection shell
Resolution (Å)Num. unique obsRrim(I) allDiffraction-IDRmerge(I) obsCC1/2
1.45-1.5491492.0951
1.54-1.6486751.95911.4820.143
1.64-1.7780871.15810.8830.365
1.77-1.9474740.56310.4260.732
1.94-2.1767860.28810.2240.916
2.17-2.557970.1910.1490.954
2.5-3.0647640.13710.1080.973
3.06-4.3237810.08910.070.986

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→45.24 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 3634 5 %
Rwork0.1472 --
obs0.149 72655 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 48 226 3395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133267
X-RAY DIFFRACTIONf_angle_d1.3294446
X-RAY DIFFRACTIONf_dihedral_angle_d13.5161217
X-RAY DIFFRACTIONf_chiral_restr0.311486
X-RAY DIFFRACTIONf_plane_restr0.019580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.36991350.33152561X-RAY DIFFRACTION98
1.47-1.490.33791370.29342602X-RAY DIFFRACTION100
1.49-1.510.30161410.26882666X-RAY DIFFRACTION100
1.51-1.530.29141360.24992587X-RAY DIFFRACTION100
1.53-1.550.33751380.23782630X-RAY DIFFRACTION100
1.55-1.580.2771380.23342619X-RAY DIFFRACTION100
1.58-1.610.27541380.2122627X-RAY DIFFRACTION100
1.61-1.640.24351390.21082634X-RAY DIFFRACTION100
1.64-1.670.25611390.20582634X-RAY DIFFRACTION100
1.67-1.70.28051370.20412608X-RAY DIFFRACTION100
1.7-1.740.23791390.18942639X-RAY DIFFRACTION100
1.74-1.780.2221390.17162652X-RAY DIFFRACTION100
1.78-1.820.21271390.15232626X-RAY DIFFRACTION100
1.82-1.870.17231390.1282659X-RAY DIFFRACTION100
1.87-1.930.16661390.12182640X-RAY DIFFRACTION100
1.93-1.990.17391390.12582635X-RAY DIFFRACTION100
1.99-2.060.17551390.13192638X-RAY DIFFRACTION100
2.06-2.140.18261410.12872685X-RAY DIFFRACTION100
2.14-2.240.1691390.11922637X-RAY DIFFRACTION100
2.24-2.360.1661400.12772662X-RAY DIFFRACTION100
2.36-2.510.17571410.13212674X-RAY DIFFRACTION100
2.51-2.70.1731410.13842686X-RAY DIFFRACTION100
2.7-2.970.16711420.14492695X-RAY DIFFRACTION100
2.97-3.40.1681420.14192702X-RAY DIFFRACTION100
3.4-4.290.15481450.12552750X-RAY DIFFRACTION100
4.29-45.240.15861520.13862873X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more