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Basic information

Entry
Database: PDB / ID: 1cel
TitleTHE THREE-DIMENSIONAL CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF CELLOBIOHYDROLASE I FROM TRICHODERMA REESEI
Components1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I
KeywordsHYDROLASE(O-GLYCOSYL)
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-D-glucopyranose / alpha-D-glucopyranose / 2-IODOBENZYLTHIO GROUP / Exoglucanase 1 / Exoglucanase 1
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsDivne, C. / Jones, T.A.
Citation
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.
#1: 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
DepositionMay 17, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn
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 2.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.conn_type_id / _struct_conn.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.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
Remark 700SHEET EACH CHAIN CONTAINS TWO LARGE ANTI-PARALLEL BETA SHEETS THAT STACK FACE-TO-FACE TO FORM A ...SHEET EACH CHAIN CONTAINS TWO LARGE ANTI-PARALLEL BETA SHEETS THAT STACK FACE-TO-FACE TO FORM A BETA SANDWICH. EACH SHEET IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE PRESENTED FOR EACH SHEET WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEET 1 OF THE SANDWICH IS PRESENTED AS SHEETS *A1A* AND *A1B* FOR CHAIN A AND SHEETS *B1A* AND *B1B* FOR CHAIN B. SHEET 2 OF THE SANDWICH IS PRESENTED AS SHEETS *A2A* AND *A2B* FOR CHAIN A AND SHEETS *B2A* AND *B2B* FOR CHAIN B. THE FOLLOWING B-STRANDS ARE DISJOINT IN THE TWO SHEETS OF THE B-SANDWICH: STRAND 2 OF SHEET 1 IS DISJOINT CONSISTING OF TWO STRANDS (RESIDUES 24 - 26 AND RESIDUES 84 - 87) THAT RUN IN OPPOSITE DIRECTIONS; STRAND 3 OF SHEET 1 IS DISJOINT CONSISTING OF TWO STRANDS (RESIDUES 17 - 20 AND RESIDUES 90 - 95) THAT RUN IN OPPOSITE DIRECTIONS; STRAND 8 OF SHEET 1 IS DISJOINT CONSISTING OF TWO STRANDS (RESIDUES 309 - 313 AND RESIDUES 325 - 327) THAT RUN IN THE SAME DIRECTION; STRAND 2 OF SHEET 2 IS DISJOINT CONSISTING OF TWO STRANDS (RESIDUES 107 - 111 AND RESIDUES 119 - 121) THAT RUN IN THE SAME DIRECTION.

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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
B: 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3649
Polymers92,0212
Non-polymers1,3437
Water9,530529
1
A: 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7025
Polymers46,0111
Non-polymers6924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6624
Polymers46,0111
Non-polymers6513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.000, 86.200, 111.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO A 382 / 2: CIS PROLINE - PRO B 382
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1) / Vector: -38.092, -43.108, -56.393)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 46010.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei (fungus)
References: UniProt: P00725, UniProt: P62694*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Sugars , 3 types, 4 molecules

#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#3: Sugar ChemComp-BGC / beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 532 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-IBZ / 2-IODOBENZYLTHIO GROUP


Mass: 250.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7IS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsA LIGAND O-IODO-BENZYL-1-THIO-B-D-GLUCOSE IS BOUND IN THE ACTIVE SITE OF EACH MOLECULE AND HAS THE ...A LIGAND O-IODO-BENZYL-1-THIO-B-D-GLUCOSE IS BOUND IN THE ACTIVE SITE OF EACH MOLECULE AND HAS THE RESIDUE NAMES IBZ AND GLC (I.E., IBZ FOR THE IODO-BENZYL GROUP AND GLC FOR THE B-D-GLUCOSE UNIT). THERE IS A CALCIUM (+II) ION COORDINATED BY GLU 295 AND GLU 325 FROM ONE MOLECULE (CHAIN A) AND GLU 295 AND GLU 325 FROM A NON-CRYSTALLOGRAPHICALLY RELATED B MOLECULE. IN ADDITION, ONE WATER MOLECULE IS BOUND TO THE CALCIUM ION. THE COORDINATION IS DISTORTED PENTAGONAL BIPYRAMIDAL.
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: GUX1_TRIRE SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLN 18 PCA A 1 GLN 18 PCA B 1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal grow
*PLUS
pH: 3.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-10 mg/mlprotein1drop0.005ml
210 mMglycine1drop
310 %PEG200001drop0.005ml
450 mMcalcium chloride1drop0.001 ml
51 mMo-iodobenzyl-1-thio-beta-D-cellobioside1drop
60.2 Msodium chloride1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.81 Å / Num. obs: 65174 / % possible obs: 95.5 % / Num. measured all: 99089 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
Highest resolution: 1.81 Å / Lowest resolution: 1.87 Å / % possible obs: 52 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→7.5 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.181 -
obs0.181 63053
Refinement stepCycle: LAST / Resolution: 1.8→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 69 529 7038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.4

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