[English] 日本語
Yorodumi
- PDB-2c24: FAMILY 30 CARBOHYDRATE-BINDING MODULE OF CELLULOSOMAL CELLULASE C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c24
TitleFAMILY 30 CARBOHYDRATE-BINDING MODULE OF CELLULOSOMAL CELLULASE CEL9D- CEL44B OF CLOSTRIDIUM THERMOCELLUM
ComponentsENDOGLUCANASE
KeywordsHYDROLASE / CBM30 / CLOSTRIDIUM THERMOCELLUM / CELLULOSOME
Function / homology
Function and homology information


cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
: / Carbohydrate binding domain 30 / Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Galactose-binding lectin / PKD domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 ...: / Carbohydrate binding domain 30 / Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Galactose-binding lectin / PKD domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsCarvalho, A.L. / Alves, V.D. / Najmudin, S. / Romao, M.J. / Prates, J.A.M. / Ferreira, L.M.A. / Bolam, D.N. / Gilbert, H.J. / Fontes, C.M.G.A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Xyloglucan is Recognized by Carbohydrate-Binding Modules that Interact with Beta-Glucan Chains.
Authors: Najmudin, S. / Guerreiro, C.I.P.D. / Carvalho, A.L. / Prates, J.A.M. / Correia, M.A.S. / Alves, V.D. / Ferreira, L.M.A. / Romao, M.J. / Gilbert, H.J. / Bolam, D.N. / Fontes, C.M.G.A.
History
DepositionSep 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOGLUCANASE
B: ENDOGLUCANASE


Theoretical massNumber of molelcules
Total (without water)46,6142
Polymers46,6142
Non-polymers00
Water3,909217
1
A: ENDOGLUCANASE


Theoretical massNumber of molelcules
Total (without water)23,3071
Polymers23,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDOGLUCANASE


Theoretical massNumber of molelcules
Total (without water)23,3071
Polymers23,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.579, 85.475, 88.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A8 - 182
2115B8 - 182

-
Components

#1: Protein ENDOGLUCANASE / FAMILY 30 CARBOHYDRATE BINDING MODULE


Mass: 23307.133 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P71140
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 60 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.072
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 24116 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.6
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WMX

1wmx


Resolution: 2.27→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.881 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2440 10.1 %RANDOM
Rwork0.216 ---
obs0.221 21633 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.27→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 0 217 2996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222845
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9423879
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6124.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64315466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1561512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1720.21178
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21976
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4661.51769
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84722804
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.77531276
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2764.51075
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
672medium positional0.090.5
675loose positional0.335
672medium thermal0.812
675loose thermal1.2810
LS refinement shellResolution: 2.27→2.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 177
Rwork0.295 1545

+
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://pdbjlvh1.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