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- PDB-1q2e: CELLOBIOHYDROLASE CEL7A WITH LOOP DELETION 245-252 AND BOUND NON-... -

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Basic information

Entry
Database: PDB / ID: 1q2e
TitleCELLOBIOHYDROLASE CEL7A WITH LOOP DELETION 245-252 AND BOUND NON-HYDROLYSABLE CELLOTETRAOSE
ComponentsEXOCELLOBIOHYDROLASE I
KeywordsHYDROLASE / CELLULASE / CELLULOSE DEGRADATION / GLYCOSIDASE / GLYCOPROTEIN / GLYCOSYLATED PROTEIN / LOOP DELETION / CELLOTETRAOSE
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
Exoglucanase 1 / Exoglucanase 1
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsStahlberg, J. / Harris, M. / Jones, T.A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Engineering the exo-loop of Trichoderma reesei cellobiohydrolase, Cel7A. A comparison with Phanerochaete chrysosporium Cel7D
Authors: von Ossowski, I. / Stahlberg, J. / Koivula, A. / Piens, K. / Becker, D. / Boer, H. / Harle, R. / Harris, M. / Divne, C. / Mahdi, S. / Zhao, Y. / Driguez, H. / Claeyssens, M. / Sinnott, M.L. / Teeri, T.T.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: High-Resolution Crystal Structures Reveal How a Cellulose Chain is Bound in the 50A Long Tunnel of Cellobiohydrolase-I from Trichoderma Reesei
Authors: Divne, C. / Stahlberg, J. / Teeri, T.T. / Jones, T.A.
History
DepositionJul 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXOCELLOBIOHYDROLASE I
B: EXOCELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0977
Polymers90,2222
Non-polymers1,8765
Water10,881604
1
A: EXOCELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0293
Polymers45,1111
Non-polymers9182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EXOCELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0694
Polymers45,1111
Non-polymers9583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.340, 84.310, 110.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein EXOCELLOBIOHYDROLASE I / E.C.3.2.1.91 / EXOGLUCANASE I / CBHI / 1 / 4-beta-cellobiohydrolase / cellulose 1 / 4-beta-cellobiosidase


Mass: 45110.777 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN 1-434 / Mutation: 245-252 DELETION
Source method: isolated from a genetically manipulated source
Details: COMPLEXED TO METHYL 4-S-BETA-CELLOBIOSYL-4-THIO-BETA-CELLOBIOSIDE
Source: (gene. exp.) Hypocrea jecorina (fungus) / Strain: QM9414 / Gene: cbh1 / Variant: VTT-D-93201 / Plasmid: PEM-F5 / Production host: Hypocrea jecorina (fungus) / Strain (production host): VTT-D-93201
References: UniProt: P00725, UniProt: P62694*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside


Type: oligosaccharide / Mass: 696.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5][a2122h-1a_1-5]/1-2-3-3/a4-b1_b4-c1*S*_c4-d1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][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.: 2
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 5000, TRIS-HCL, ETHYLENE GLYCOL, CALCIUM CHLORIDE, SODIUM ACETATE, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11-5 mg/mlprotein1drop
210 mMsodium acetate1droppH5.0
318-22 %(w/v)mPEG50001reservoir
40.1 Msodium morpholine ethane sulphonic acid1reservoirpH6.0
510 mM1reservoirCoCl2
612.5 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 21, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 78914 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.132 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 40 Å / Redundancy: 4.1 %
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 3.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2320 2.9 %RANDOM
Rwork0.226 ---
obs-78914 100 %-
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 121 604 7037
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 76597 / % reflection Rfree: 2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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