[English] 日本語
Yorodumi
- PDB-1exp: BETA-1,4-GLYCANASE CEX-CD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1exp
TitleBETA-1,4-GLYCANASE CEX-CD
ComponentsBETA-1,4-D-GLYCANASE CEX-CD
KeywordsHYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDASE
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process
Similarity search - Function
Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 ...Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-deoxy-2-fluoro-beta-cellobiose / : / Exoglucanase/xylanase
Similarity search - Component
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsWhite, A. / Tull, D. / Johns, K.L. / Withers, S.G. / Rose, D.R.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase.
Authors: White, A. / Tull, D. / Johns, K. / Withers, S.G. / Rose, D.R.
#1: Journal: Biochemistry / Year: 1994
Title: Crystal Structure of the Catalytic Domain of the Beta-1,4-Glycanase Cex from Cellulomonas Fimi
Authors: White, A. / Withers, S.G. / Gilkes, N.R. / Rose, D.R.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of the Catalytic Domain of Cex, an Exo-Beta-1,4-Glucanase and Beta-1,4-Xylanase from the Bacterium Cellulomonas Fimi
Authors: Bedarkar, S. / Gilkes, N.R. / Kilburn, D.G. / Kwan, E. / Rose, D.R. / Miller Junior, R.C. / Warren, R.A. / Withers, S.G.
History
DepositionJan 11, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-1,4-D-GLYCANASE CEX-CD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3962
Polymers34,0521
Non-polymers3441
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.172, 88.172, 81.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

-
Components

#1: Protein BETA-1,4-D-GLYCANASE CEX-CD / CELLOBIOHYDROLASE/XYLANASE B


Mass: 34051.941 Da / Num. of mol.: 1 / Fragment: CATALYTICALLY ACTIVE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (bacteria) / Production host: Escherichia coli (E. coli)
References: GenBank: 144429, UniProt: P07986*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end), endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 344.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2-deoxy-2-fluoro-beta-cellobiose
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*F][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp2fluoro]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop / Details: Bedarkar, S., (1992) J.Mol. Biol, 228, 693.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
165 mg/mlCex1dropin water
27.5-10 %PEG40001drop
30.1 Msodium acetate1drop
47.5-10 %PEG40001reservoir
50.1 Msodium acetate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 29109 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.041
Reflection
*PLUS
Lowest resolution: 8 Å / Num. obs: 29464 / Num. measured all: 139457

-
Processing

Software
NameVersionClassification
SDMWHOWARD & NEILSONdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSDETECTOR SYSTEM (NIELSEN)data reduction
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.283 -7 %
Rwork0.208 --
obs0.208 26463 90 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 22 189 2607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 24597
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

+
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