[English] 日本語
Yorodumi
- PDB-9w4f: Crystal structure of beta-glucosidase CaBGL mutant E163Q in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9w4f
TitleCrystal structure of beta-glucosidase CaBGL mutant E163Q in complex with glucose
Componentsbeta-glucosidase
KeywordsHYDROLASE / CaBGL / cellulose saccharification / Caldicellulosiruptor sp. F32
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / beta-glucosidase
Similarity search - Component
Biological speciesCaldicellulosiruptor sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsYou, C. / Feng, Y.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200030 China
National Natural Science Foundation of China (NSFC)32170051 China
CitationJournal: Bioresour Technol / Year: 2025
Title: Engineering of beta-glucosidase CaBGL with improved performance in cellulose hydrolysis.
Authors: You, C. / Zheng, X. / Qi, K. / Dong, S. / Liu, Y.J. / Chen, C. / Cui, Q. / Feng, Y.
History
DepositionJul 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: beta-glucosidase
B: beta-glucosidase
C: beta-glucosidase
D: beta-glucosidase
E: beta-glucosidase
F: beta-glucosidase
G: beta-glucosidase
H: beta-glucosidase
I: beta-glucosidase
J: beta-glucosidase
K: beta-glucosidase
L: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)648,24061
Polymers642,75112
Non-polymers5,48849
Water17,294960
1
A: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1196
Polymers53,5631
Non-polymers5565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9395
Polymers53,5631
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9395
Polymers53,5631
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.030, 221.580, 236.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
beta-glucosidase / beta-glucosidase CaBGL


Mass: 53562.586 Da / Num. of mol.: 12 / Mutation: E163Q
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Caldicellulosiruptor sp. is not available during the biocuration, replaced by I7DLX2 temporarily.
Source: (gene. exp.) Caldicellulosiruptor sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: I7DLX2, beta-glucosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 10 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 960 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.1M Bis-Tris, pH 6.5, 2.0 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.26→36.92 Å / Num. obs: 339559 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Χ2: 0.96 / Net I/σ(I): 17.7
Reflection shellResolution: 2.26→2.32 Å / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.607 / Num. measured all: 163276 / Num. unique obs: 24959 / CC1/2: 0.881 / Rpim(I) all: 0.257 / Rrim(I) all: 0.66 / Χ2: 0.87 / Net I/σ(I) obs: 3.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→36.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.199 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 17163 5.1 %RANDOM
Rwork0.20266 ---
obs0.20371 322272 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.911 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---1.66 Å20 Å2
3---2.21 Å2
Refinement stepCycle: 1 / Resolution: 2.26→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45436 0 330 960 46726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01247071
X-RAY DIFFRACTIONr_bond_other_d0.0020.01643083
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.81163808
X-RAY DIFFRACTIONr_angle_other_deg0.5051.76799043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71455422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.2265204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.002107888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.26543
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0255566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211758
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_it4.2924.48821724
X-RAY DIFFRACTIONr_mcbond_other4.2914.48821724
X-RAY DIFFRACTIONr_mcangle_it5.8398.04327134
X-RAY DIFFRACTIONr_mcangle_other5.8398.04327135
X-RAY DIFFRACTIONr_scbond_it5.1324.97525347
X-RAY DIFFRACTIONr_scbond_other5.1284.97425340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6588.88836663
X-RAY DIFFRACTIONr_long_range_B_refined9.80255.07218617
X-RAY DIFFRACTIONr_long_range_B_other9.80255.07218615
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 1275 -
Rwork0.274 23581 -
obs--99.99 %

+
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