[English] 日本語
Yorodumi
- PDB-1g9j: X-TAL STRUCTURE OF THE MUTANT E44Q OF THE CELLULASE CEL48F IN COM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g9j
TitleX-TAL STRUCTURE OF THE MUTANT E44Q OF THE CELLULASE CEL48F IN COMPLEX WITH A THIOOLIGOSACCHARIDE
ComponentsCELLULASE CEL48F
KeywordsHYDROLASE / alpha-alpha-6-barrel / cellulase / thiooligosaccharide
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Endo-1,4-beta-glucanase f; domain 3 / Endo-1,4-beta-glucanase f. Domain 3 / Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain ...Endo-1,4-beta-glucanase f; domain 3 / Endo-1,4-beta-glucanase f. Domain 3 / Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / EF-hand calcium-binding domain. / Few Secondary Structures / Irregular / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesClostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsParsiegla, G. / Tardif, C. / Belaich, J.P. / Driguez, H. / Haser, R.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structures of mutants of cellulase Cel48F of Clostridium cellulolyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action
Authors: Parsiegla, G. / Reverbel, C. / Tardif, C. / Driguez, H. / Haser, R.
#1: Journal: Biochemistry / Year: 2000
Title: Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action.
Authors: Parsiegla, G. / Reverbel-Leroy, C. / Tardif, C. / Belaich, J.P. / Driguez, H. / Haser, R.
#2: Journal: Embo J. / Year: 1998
Title: The crystal structure of the processive endocellulase CelF of Clostridium cellullolyticum in complex with a thiooligosaccharide inhibitor at 2.0 resolution.
Authors: Parsiegla, G. / Juy, M. / Reverbel-Leroy, C. / Tardif, C. / Belaich, J.P. / Driguez, H. / Haser, R.
History
DepositionNov 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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_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_struct_assembly_gen.asym_id_list / _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.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.value / _struct_conn.pdbx_dist_value / _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
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CELLULASE CEL48F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3645
Polymers70,8691
Non-polymers1,4954
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.480, 84.720, 121.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CELLULASE CEL48F


Mass: 70868.891 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE / Mutation: E44Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37698, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta- ...beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1379.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/1,8,7/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1/a4-b1*S*_b4-c1_c4-d1*S*_d4-e1_e4-f1*S*_f4-g1_g4-h1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{}}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, PEG 4000, CaCl2, thiooligosaccharide IG12, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reverbel-Leroy, C., (1997) Acta Crystallogr., D.54, 114.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
22 mMIG41drop
30.5 M1reservoiror 0.3MNaCl
4PEG40001drop

-
Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FU581 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 2000 / Details: Osmic confocal mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 50753 / Num. obs: 45078 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.7 / Num. unique all: 12065 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 1.9→49.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2100897.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2585 5.1 %OTHER
Rwork0.182 ---
obs0.182 50697 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.67 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---2.6 Å20 Å2
3---2.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5101 0 92 375 5568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.521.5
X-RAY DIFFRACTIONc_mcangle_it0.892
X-RAY DIFFRACTIONc_scbond_it0.932
X-RAY DIFFRACTIONc_scangle_it1.42.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 419 5 %
Rwork0.255 7880 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

+
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