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- PDB-1ut9: Structural Basis for the Exocellulase Activity of the Cellobiohyd... -

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Basic information

Entry
Database: PDB / ID: 1ut9
TitleStructural Basis for the Exocellulase Activity of the Cellobiohydrolase CbhA from C. thermocellum
ComponentsCELLULOSE 1,4-BETA-CELLOBIOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / FAMILY 9 / CELLOBIOHYDROLASE
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase activity / cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
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. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily ...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. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.1 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: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_radiation / entity_src_gen / exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_detector.detector / _diffrn_detector.type / _diffrn_radiation.pdbx_diffrn_protocol / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _exptl_crystal_grow.method
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELLULOSE 1,4-BETA-CELLOBIOSIDASE


Theoretical massNumber of molelcules
Total (without water)68,6081
Polymers68,6081
Non-polymers00
Water15,493860
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.546, 75.760, 137.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CELLULOSE 1,4-BETA-CELLOBIOSIDASE / CELLOBIOHYDROLASE CBHA / EXOGLUCANASE / EXOCELLOBIOHYDROLASE / 1 / 4-BETA-CELLOBIOHYDROLASE


Mass: 68608.016 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 208-816
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Plasmid: PET-21B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6RSN8*PLUS, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 %
Crystal growMethod: batch mode / pH: 8.5 / Details: 20% PEG4000, 0.2M (NH4)2SO4, 0.1M TRIS, PH 7.0
Crystal grow
*PLUS
Temperature: 273 K / pH: 8.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
225 mMTris-HCl1droppH8.5
30.2 M1dropNaCl
420 %PEG40001reservoir
50.2 Mammonium sulfate1reservoir
60.1 MTris1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: RIGAKU HI RES OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→69 Å / Num. obs: 41182 / % possible obs: 92 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 66
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 69 Å / % possible obs: 91.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 65.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
REFMACrefinement
PROTEUMdata reduction
PROTEUMdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.1→69.01 Å / SU B: 3.621 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PLEASE NOTE THAT THIS ENTRY CONTAINS ATOMS REFINED WITH 0.00 OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18553 2190 5 %RANDOM
Rwork0.14732 ---
obs0.14928 41182 93.82 %-
Displacement parametersBiso mean: 17.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.31 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4809 0 0 860 5669
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 69 Å / Rfactor Rfree: 0.185 / Rfactor Rwork: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.008
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.381

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