[English] 日本語
Yorodumi
- PDB-8xi1: Cellodextrin phosphorylase from Clostridium thermocellum mutant -... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xi1
TitleCellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines
Componentscellodextrin phosphorylase variant
KeywordsCARBOHYDRATE / Cellulose / Cellodextrin / Synthesis / Phosphorolysis
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsKuga, T. / Sunagawa, N. / Igarashi, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J12566 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H05494 Japan
CitationJournal: J Appl Glycosci (1999) / Year: 2024
Title: Effect of Free Cysteine Residues to Serine Mutation on Cellodextrin Phosphorylase.
Authors: Kuga, T. / Sunagawa, N. / Igarashi, K.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 25, 2024ID: 8H2K
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: pdbx_database_related
Revision 1.2Jul 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cellodextrin phosphorylase variant
B: cellodextrin phosphorylase variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,15214
Polymers225,3582
Non-polymers79312
Water45,5242527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-81 kcal/mol
Surface area69130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.441, 89.048, 88.989
Angle α, β, γ (deg.)98.884, 110.547, 110.674
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein cellodextrin phosphorylase variant


Mass: 112679.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Strain: YM4 / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 5 types, 2539 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2527 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10 mg/ml protein solution was mixed 1:1 with an optimized solution consisting of 100 mM pH 5.0 sodium acetate, 12% PEG4000, and 5% glycerol with streak seeding

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→43.76 Å / Num. obs: 418204 / % possible obs: 93.49 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.99
Reflection shellResolution: 1.37→1.419 Å / Mean I/σ(I) obs: 1.21 / Num. unique obs: 41686 / CC1/2: 0.558

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
PHENIXphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→43.76 Å / SU ML: 0.1835 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.3928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2001 21009 5.02 %
Rwork0.1743 397158 -
obs0.1756 418168 93.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.39 Å2
Refinement stepCycle: LAST / Resolution: 1.37→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15746 0 47 2527 18320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008316700
X-RAY DIFFRACTIONf_angle_d0.957722662
X-RAY DIFFRACTIONf_chiral_restr0.0782458
X-RAY DIFFRACTIONf_plane_restr0.00892969
X-RAY DIFFRACTIONf_dihedral_angle_d14.30196185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.3777080.36913132X-RAY DIFFRACTION93.15
1.39-1.40.36286970.343113223X-RAY DIFFRACTION93.24
1.4-1.420.31927210.318713192X-RAY DIFFRACTION93.39
1.42-1.440.32336580.301313274X-RAY DIFFRACTION93.64
1.44-1.460.27766270.264813313X-RAY DIFFRACTION93.64
1.46-1.480.27276970.244313280X-RAY DIFFRACTION93.84
1.48-1.50.27146870.241613349X-RAY DIFFRACTION93.98
1.5-1.520.25517000.220413287X-RAY DIFFRACTION94.06
1.52-1.540.24136540.221913453X-RAY DIFFRACTION94.23
1.54-1.570.25516090.225213452X-RAY DIFFRACTION94.39
1.57-1.60.2376960.221713394X-RAY DIFFRACTION94.53
1.6-1.620.22447370.203413263X-RAY DIFFRACTION93.91
1.62-1.660.24387510.20113236X-RAY DIFFRACTION93.8
1.66-1.690.2297100.196713419X-RAY DIFFRACTION94.58
1.69-1.730.22456790.189113453X-RAY DIFFRACTION94.74
1.73-1.770.21097270.189913304X-RAY DIFFRACTION94.53
1.77-1.810.22417900.183913373X-RAY DIFFRACTION94.35
1.81-1.860.2087050.187713304X-RAY DIFFRACTION94.14
1.86-1.910.23147400.212713124X-RAY DIFFRACTION93.11
1.91-1.980.25377000.222313074X-RAY DIFFRACTION92.16
1.98-2.050.17897400.169113139X-RAY DIFFRACTION93.28
2.05-2.130.18586490.162813299X-RAY DIFFRACTION93.14
2.13-2.230.18836870.166913090X-RAY DIFFRACTION92.54
2.23-2.340.24336690.18812379X-RAY DIFFRACTION87.42
2.34-2.490.1886790.15113142X-RAY DIFFRACTION92.9
2.49-2.680.20016720.151113191X-RAY DIFFRACTION92.97
2.68-2.950.18677370.153413137X-RAY DIFFRACTION92.99
2.95-3.380.17257490.143413232X-RAY DIFFRACTION93.85
3.38-4.260.14787530.132813293X-RAY DIFFRACTION94.1
4.26-43.760.16736810.151913357X-RAY DIFFRACTION94.13

+
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