[English] 日本語
Yorodumi
- PDB-9g4n: Glycoside Hydrolase Family 157 from Labilibaculum antarcticum (La... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g4n
TitleGlycoside Hydrolase Family 157 from Labilibaculum antarcticum (LaGH157) E224A mutant in complex with Laminaritriose and Glucose
ComponentsGlycoside hydrolase family 2 catalytic domain-containing protein
KeywordsHYDROLASE / GH157 / endo-1 / 3(4)-beta-glucanase / Labilibaculum antarcticum / glycoside hydrolase
Function / homologyGlycoside hydrolase superfamily / beta-D-glucopyranose / TRIETHYLENE GLYCOL / Glycoside hydrolase family 2 catalytic domain-containing protein
Function and homology information
Biological speciesLabilibaculum antarcticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsCaseiro, C. / Alves, V.D. / Carvalho, A.L. / Bule, P.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)SFRH/BD/147152/2019 Portugal
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Family GH157 enzyme exhibits broad linkage tolerance and a dual endo/exo-beta-glucanase activity on beta-glucans.
Authors: Caseiro, C. / McGregor, N.G.S. / Alves, V.D. / Carvalho, A.L. / Romao, M.J. / Davies, G.J. / Fontes, C.M.G.A. / Bule, P.
History
DepositionJul 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoside hydrolase family 2 catalytic domain-containing protein
B: Glycoside hydrolase family 2 catalytic domain-containing protein
C: Glycoside hydrolase family 2 catalytic domain-containing protein
D: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,76427
Polymers245,8244
Non-polymers3,94023
Water17,457969
1
A: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2955
Polymers61,4561
Non-polymers8394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5418
Polymers61,4561
Non-polymers1,0857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2655
Polymers61,4561
Non-polymers8094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6639
Polymers61,4561
Non-polymers1,2078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.854, 127.548, 171.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycoside hydrolase family 2 catalytic domain-containing protein


Mass: 61456.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Labilibaculum antarcticum (bacteria) / Gene: ALGA_4297 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1CQ89

-
Sugars , 2 types, 7 molecules

#2: Polysaccharide
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3 / 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

-
Non-polymers , 4 types, 985 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0,1 M Sodium Malonate pH4, 10% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.32→47.71 Å / Num. obs: 109278 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.069 / Rrim(I) all: 0.204 / Χ2: 0.99 / Net I/σ(I): 8.3 / Num. measured all: 929935
Reflection shellResolution: 2.32→2.4 Å / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 2.056 / Num. measured all: 94107 / Num. unique obs: 10641 / CC1/2: 0.629 / Rpim(I) all: 0.72 / Rrim(I) all: 2.18 / Χ2: 0.82 / Net I/σ(I) obs: 1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→47.71 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.011 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24718 5264 4.8 %RANDOM
Rwork0.20453 ---
obs0.20659 103930 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.698 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å20 Å2
2---0.27 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.32→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16954 0 262 969 18185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01217616
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616304
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.82123812
X-RAY DIFFRACTIONr_angle_other_deg0.5751.77637872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.66352107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.285544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.702103103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.22584
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0220144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023832
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6941.9948434
X-RAY DIFFRACTIONr_mcbond_other1.6931.9948434
X-RAY DIFFRACTIONr_mcangle_it2.6023.57910536
X-RAY DIFFRACTIONr_mcangle_other2.6023.5810537
X-RAY DIFFRACTIONr_scbond_it2.2642.2269182
X-RAY DIFFRACTIONr_scbond_other2.2642.2279183
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5163.98113276
X-RAY DIFFRACTIONr_long_range_B_refined5.14821.3319896
X-RAY DIFFRACTIONr_long_range_B_other5.1320.6119684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.622 338 -
Rwork0.581 7657 -
obs--99.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54320.04460.21351.01210.01850.63640.0605-0.04710.01730.1303-0.03560.03960.0043-0.0768-0.0250.0425-0.00990.03110.0116-0.00120.2293-67.6115.104-76.675
20.51270.0049-0.06220.6997-0.05241.19230.013-0.0273-0.02450.08160.00250.00660.0389-0.0555-0.01550.0271-0.00210.00660.00460.00950.2686-19.006-4.412-65.694
30.7181-0.11760.06941.4149-0.23940.6392-0.0169-0.08930.02180.43810.0620.0687-0.17630.0108-0.0450.22350.00570.00730.01490.00870.2175-19.99455.258-54.978
40.46350.03540.02160.7379-0.32560.89560.00370.0113-0.0249-0.08690.02590.06440.0502-0.0623-0.02960.029-0.0053-0.02940.0061-0.01370.2668-49.00210.81-19.605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 530
2X-RAY DIFFRACTION2B3 - 529
3X-RAY DIFFRACTION3C3 - 529
4X-RAY DIFFRACTION4D3 - 529

+
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