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- PDB-1rq5: Structural Basis for the Exocellulase Activity of the Cellobiohyd... -

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Basic information

Entry
Database: PDB / ID: 1rq5
TitleStructural Basis for the Exocellulase Activity of the Cellobiohydrolase CbhA from C. thermocellum
ComponentsCellobiohydrolase
KeywordsHYDROLASE / Cellobiohydrolase / CbhA / EXOCELLULASE / FAMILY 9
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Bacterial Ig domain / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 ...Bacterial Ig domain / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyltransferase - #10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-cellotetraose / Glucanase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchubot, F.D. / Kataeva, I.A. / Chang, J. / Shah, A.K. / Ljungdahl, L.G. / Rose, J.P. / Wang, B.C.
CitationJournal: Biochemistry / Year: 2004
Title: Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum
Authors: Schubot, F.D. / Kataeva, I.A. / Chang, J. / Shah, A.K. / Ljungdahl, L.G. / Rose, J.P. / Wang, B.C.
History
DepositionDec 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_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 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 600HETEROGEN ATOM O1X IS MISSING FOR THE LIGAND LABELED CTT.
Remark 999 SEQUENCE THE AUTHOR STATES THAT RESIDUES 814 TO 817 ARE PART OF THE NATIVE PROTEIN AS SHOWN IN ... SEQUENCE THE AUTHOR STATES THAT RESIDUES 814 TO 817 ARE PART OF THE NATIVE PROTEIN AS SHOWN IN GENBANK ENTRY CAA56918, BUT WERE OMITTED WHEN THE PROTEIN WAS RESEQUENCED TO GENBANK ENTRY AAR87745

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4534
Polymers68,7061
Non-polymers7473
Water6,972387
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.600, 108.600, 119.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Cellobiohydrolase


Mass: 68706.117 Da / Num. of mol.: 1 / Mutation: E796Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Plasmid: PET-21B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21
References: UniProt: Q59325, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M SrCl2, 20% PEG4000, 0.2M (NH4)2SO4, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jul 10, 2002 / Details: Rigaku Hi Res optics
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→54 Å / Num. all: 35372 / Num. obs: 29695 / % possible obs: 84 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.24 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PROTEUM PLUSsoftware packagedata collection
PROTEUM PLUSsoftware packagedata reduction
CNSrefinement
PROTEUM PLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE OF Ig-GH9_CbhA

Resolution: 2.4→20 Å / Isotropic thermal model: Isotropic / σ(F): 1.5 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1238 -RANDOM
Rwork0.21 ---
all0.23 35372 --
obs0.21 25481 72 %-
Solvent computationBsol: 32.6499 Å2 / ksol: 0.302098 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.623 Å2-2.315 Å20 Å2
2--2.623 Å20 Å2
3----5.245 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 47 387 5223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009286
X-RAY DIFFRACTIONc_angle_deg1.85779
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ctt.par

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