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- PDB-4cel: ACTIVE-SITE MUTANT D214N DETERMINED AT PH 6.0 WITH NO LIGAND BOUN... -

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Basic information

Entry
Database: PDB / ID: 4cel
TitleACTIVE-SITE MUTANT D214N DETERMINED AT PH 6.0 WITH NO LIGAND BOUND IN THE ACTIVE SITE
Components1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE ICellulose 1,4-beta-cellobiosidase
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
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.2 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: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._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 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
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_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_auth_seq_id / _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 / _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 2.2Nov 3, 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

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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)92,7388
Polymers92,1362
Non-polymers6036
Water7,855436
1
A: 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3694
Polymers46,0681
Non-polymers3013
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)46,3694
Polymers46,0681
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.000, 86.200, 111.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999941, -0.010745, 0.001368), (0.010751, 0.999932, -0.004552), (-0.001319, 0.004567, 0.999989)
Vector: -38.5007, -43.1056, -56.0724)
DetailsTHERE ARE TWO COPIES OF THE MOLECULE IN THE ASYMMETRIC UNIT. NON-CRYSTALLOGRAPHIC CONSTRAINTS HAVE BEEN APPLIED DURING REFINEMENT.

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Components

#1: Protein 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I / Cellulose 1,4-beta-cellobiosidase / EXOGLUCANASE


Mass: 46067.750 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 1 - 434 / Mutation: D214N
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: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: 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 / N-Acetylglucosamine


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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE IS A CALCIUM (+II) COUNTER ION COORDINATED BY GLU 295 AND GLU 325 FROM ONE MOLECULE, TOGETHER ...THERE IS A CALCIUM (+II) COUNTER ION COORDINATED BY GLU 295 AND GLU 325 FROM ONE MOLECULE, TOGETHER WITH GLU 295 AND GLU 395 FROM AN NCS-RELATED MOLECULE. THERE IS ALSO ONE WATER MOLECULE BOUND TO THE CALCIUM ION. THE COORDINATION IS DISTORTED PENTAGONAL BIPYRAMIDAL. THIS SITE IS PRESENTED AS SITE CAL.

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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: 4.5 MM MES PH 6.0, 9% PEG 6000, 4.5 MM CACL2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
24.5 mMMES1drop
39 %(w/v)PEG60001drop
44.5 mM1dropCaCl2
50.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 15, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→46.6 Å / Num. obs: 41627 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.5 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 143220
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementResolution: 2.2→7.5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.239 4175 10 %
Rwork0.206 --
obs0.206 40447 -
Displacement parametersBiso mean: 17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6448 0 32 436 6916
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_deg1.4
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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