[English] 日本語
Yorodumi
- PDB-1g0c: ALKALINE CELLULASE K CATALYTIC DOMAIN-CELLOBIOSE COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g0c
TitleALKALINE CELLULASE K CATALYTIC DOMAIN-CELLOBIOSE COMPLEX
ComponentsENDOGLUCANASECellulase
KeywordsHYDROLASE / Alpha/beta barrel / TIM-barrel / cellobiose complex
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily ...Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / ACETIC ACID / : / Endoglucanase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsShirai, T. / Ishida, H. / Noda, J. / Yamane, T. / Ozaki, K. / Hakamada, Y. / Ito, S.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme.
Authors: Shirai, T. / Ishida, H. / Noda, J. / Yamane, T. / Ozaki, K. / Hakamada, Y. / Ito, S.
History
DepositionOct 5, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
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_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,07416
Polymers40,3671
Non-polymers1,70715
Water8,539474
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.9, 97.9, 121.6
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-594-

CD

-
Components

#1: Protein ENDOGLUCANASE / Cellulase


Mass: 40367.254 Da / Num. of mol.: 1 / Fragment: ALKALINE CELLULASE K CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: KSM-635 / Plasmid: PHSP-BC115B / Production host: Bacillus subtilis (bacteria) / References: UniProt: P19424, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.17 Å3/Da / Density % sol: 70.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Cadmium sulfate hydrate, sodium acetate, HEPES, cellobiose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %(w/v)protein1drop
220 mMcadmium sulfate hydrate1drop
30.5 Msodium acetate1drop
40.1 MHEPES1drop
540 mMcadmium sulfate hydrate1reservoir
61.0 Msodium acetate1reservoir
70.1 MHEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→8 Å / Num. all: 53676 / Num. obs: 47889 / % possible obs: 89.2 % / Observed criterion σ(I): 1 / Redundancy: 27.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.187 / % possible all: 72.4
Reflection
*PLUS
Lowest resolution: 40 Å / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 72.4 % / Num. unique obs: 3826 / Mean I/σ(I) obs: 4.9

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2339 -random
Rwork0.181 ---
all-53676 --
obs-46786 87.2 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 49 474 3319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_torsion_deg23.5
X-RAY DIFFRACTIONx_torsion_impr_deg2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 5 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Rfactor Rfree: 0.242 / Num. reflection Rfree: 191 / % reflection Rfree: 5 % / Num. reflection obs: 3807 / Rfactor all: 0.24

+
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