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- PDB-3cel: ACTIVE-SITE MUTANT E212Q DETERMINED AT PH 6.0 WITH CELLOBIOSE BOU... -

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Basic information

Entry
Database: PDB / ID: 3cel
TitleACTIVE-SITE MUTANT E212Q DETERMINED AT PH 6.0 WITH CELLOBIOSE BOUND IN THE ACTIVE SITE
Components1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I
KeywordsHYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDASE / GLYCOPROTEIN
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region
Similarity search - Function
1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. ...1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
beta-cellobiose / : / Exoglucanase 1 / Exoglucanase 1
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDivne, C. / Stahlberg, J. / Jones, T.A.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Activity studies and crystal structures of catalytically deficient mutants of cellobiohydrolase I from Trichoderma reesei.
Authors: Stahlberg, J. / Divne, C. / Koivula, A. / Piens, K. / Claeyssens, M. / Teeri, T.T. / Jones, T.A.
#1: Journal: Science / Year: 1994
Title: The Three-Dimensional Crystal Structure of the Catalytic Core of Cellobiohydrolase I from Trichoderma Reesei
Authors: Divne, C. / Stahlberg, J. / Reinikainen, T. / Ruohonen, L. / Pettersson, G. / Knowles, J.K. / Teeri, T.T. / Jones, T.A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Studies on the Core Proteins of Cellobiohydrolase I and Endoglucanase I from Trichoderma Reesei
Authors: Divne, C. / Sinning, I. / Stahlberg, J. / Pettersson, G. / Bailey, M. / Siika-Aho, M. / Margolles-Clark, E. / Teeri, T. / Jones, T.A.
History
DepositionAug 24, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence
Category: atom_site / chem_comp ...atom_site / chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _atom_site.occupancy / _chem_comp.type ..._atom_site.occupancy / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_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_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 3, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1938
Polymers46,0681
Non-polymers1,1267
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.000, 84.100, 111.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1000-

CD

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Components

#1: Protein 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I / EXOGLUCANASE / EXOCELLULASE


Mass: 46067.754 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1 - 434 / Mutation: E212Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (fungus) / Strain: QM 9414 / Gene: CBH1 / Variant: VTT-D-93201 / Plasmid: PEM-F5 / Gene (production host): CBH1 / Production host: Hypocrea jecorina (fungus)
References: UniProt: P00725, UniProt: P62694*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#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
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE I222 CRYSTAL FORM DESCRIBED HERE REPRESENTS THE HIGHER SYMMETRY EQUIVALENT TO THE PSEUDO-I222 ...THE I222 CRYSTAL FORM DESCRIBED HERE REPRESENTS THE HIGHER SYMMETRY EQUIVALENT TO THE PSEUDO-I222 PRIMITIVE ORTHORHOMBIC CELL DESCRIBED PREVIOUSLY FOR CELLOBIOHYDROLASE I.
Has protein modificationY
Nonpolymer detailsTHERE IS A CADMIUM (+II) COUNTER ION COORDINATED BY GLU 295 AND GLU 325 FROM ONE MOLECULE, TOGETHER ...THERE IS A CADMIUM (+II) COUNTER ION COORDINATED BY GLU 295 AND GLU 325 FROM ONE MOLECULE, TOGETHER WITH GLU 295 AND GLU 395 FROM A CRYSTALLOGRAPHICALLY RELATED MOLECULE. THE ENVIRONMENT AROUND THE COUNTER ION IS VERY SIMILAR TO THAT OBSERVED FOR THE P21212 CRYSTAL FORM. THIS SITE IS AS SITE CAD.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 40 %
Crystal growpH: 6
Details: 50 MM MES PH 6.0, 5% MONOMETHYL ETHER PEG 5000, 5 MM CDCL2, 1 MM CELLOBIOSE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
21 mMcellobiose1drop
35 %mPEG50001drop
45 mM1dropCdCl2
50.02 %(w/v)sodium azide1drop
650 mMMES1drop
7100 mMMES1reservoir
810 %mPEG50001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 6, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→67.1 Å / Num. obs: 26782 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 5.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 4.1 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 138916
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementResolution: 2→7.5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.256 2725 10 %
Rwork0.2 --
obs0.2 26274 -
Displacement parametersBiso mean: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 2→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 42 232 3498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
Refine LS restraints NCSNCS model details: STRICT NCS CONSTRAINTS
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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