[English] 日本語
Yorodumi
- PDB-9nxj: The GH43 domain of an alpha-l-arabinofuranosidase (AtAbf43C_GH43)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nxj
TitleThe GH43 domain of an alpha-l-arabinofuranosidase (AtAbf43C_GH43) from Acetivibrio thermocellus DSM1313
ComponentsGlycoside hydrolase family 43
KeywordsHYDROLASE / FIVE-BLADED BETA PROPELLER / BETA-TREFOIL / FUROSIDASE
Function / homology
Function and homology information


L-arabinose metabolic process / alpha-L-arabinofuranosidase activity / polysaccharide catabolic process
Similarity search - Function
Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat ...Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily
Similarity search - Domain/homology
alpha-L-arabinofuranose / Glycoside hydrolase family 43
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsGalindo, J.L. / Jeffrey, P.D. / Conway, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateEnergy Research Fund administered by the Andlinger Center for Energy and the Environment at Princeton University United States
CitationJournal: Biochem.J. / Year: 2025
Title: Functional and structural characterization of AtAbf43C: An exo-1,5-alpha-L-arabinofuranosidase from Acetivibrio thermocellus DSM1313.
Authors: Galindo, J.L. / Jeffrey, P.D. / Zhu, A. / Link, A.J. / Conway, J.M.
History
DepositionMar 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoside hydrolase family 43
B: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8918
Polymers76,2072
Non-polymers6856
Water1,58588
1
A: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5425
Polymers38,1031
Non-polymers4384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3503
Polymers38,1031
Non-polymers2462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.304, 105.304, 128.856
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVAL(chain 'A' and (resid 149 through 163 or resid 165...AA149 - 1633 - 17
12ARGARGILEILE(chain 'A' and (resid 149 through 163 or resid 165...AA165 - 33819 - 192
13ALAALAPROPRO(chain 'A' and (resid 149 through 163 or resid 165...AA341 - 474195 - 328
14AHRAHRAHRAHR(chain 'A' and (resid 149 through 163 or resid 165...AC501
25PROPROVALVAL(chain 'B' and (resid 149 through 163 or resid 165...BB149 - 1633 - 17
26ARGARGILEILE(chain 'B' and (resid 149 through 163 or resid 165...BB164 - 33818 - 192
27ALAALAPROPRO(chain 'B' and (resid 149 through 163 or resid 165...BB341 - 473195 - 327
28AHRAHRAHRAHR(chain 'B' and (resid 149 through 163 or resid 165...BG501

-
Components

#1: Protein Glycoside hydrolase family 43


Mass: 38103.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: Cthe_2138 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DHB3
#2: Sugar ChemComp-AHR / alpha-L-arabinofuranose / alpha-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
LArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinofuranoseCOMMON NAMEGMML 1.0
a-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEGmme 5000, pH 5.5 Bis-Tris, AmS04

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92015 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92015 Å / Relative weight: 1
ReflectionResolution: 2.32→29.59 Å / Num. obs: 35192 / % possible obs: 99.7 % / Redundancy: 20.6 % / Biso Wilson estimate: 41.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.027 / Rrim(I) all: 0.121 / Χ2: 0.98 / Net I/σ(I): 21.2 / Num. measured all: 724982
Reflection shellResolution: 2.32→2.38 Å / % possible obs: 96.1 % / Redundancy: 20.2 % / Rmerge(I) obs: 0.852 / Num. measured all: 50475 / Num. unique obs: 2503 / CC1/2: 0.867 / Rpim(I) all: 0.192 / Rrim(I) all: 0.874 / Χ2: 0.54 / Net I/σ(I) obs: 3.3

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→29.59 Å / SU ML: 0.3461 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.8714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1644 4.76 %
Rwork0.2027 32864 -
obs0.2049 34508 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.99 Å2
Refinement stepCycle: LAST / Resolution: 2.32→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5192 0 40 88 5320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085408
X-RAY DIFFRACTIONf_angle_d0.99187396
X-RAY DIFFRACTIONf_chiral_restr0.0609788
X-RAY DIFFRACTIONf_plane_restr0.007950
X-RAY DIFFRACTIONf_dihedral_angle_d18.83211943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.36661470.29152578X-RAY DIFFRACTION93.29
2.38-2.460.35951100.27392692X-RAY DIFFRACTION96.02
2.46-2.550.35021550.26952706X-RAY DIFFRACTION97.05
2.55-2.650.35631300.25422712X-RAY DIFFRACTION97.4
2.65-2.770.31351350.25432724X-RAY DIFFRACTION97.08
2.77-2.920.30661310.24752691X-RAY DIFFRACTION97.18
2.92-3.10.27171570.24042761X-RAY DIFFRACTION98.65
3.1-3.340.31471140.23352779X-RAY DIFFRACTION99.31
3.34-3.670.2631290.21242797X-RAY DIFFRACTION99.59
3.67-4.20.22151560.18032791X-RAY DIFFRACTION99.7
4.2-5.290.17591420.14642797X-RAY DIFFRACTION99.8
5.29-29.590.18311380.16372836X-RAY DIFFRACTION99.77

+
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