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- PDB-7cbd: Catalytic domain of Cellulomonas fimi Cel6B -

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Basic information

Entry
Database: PDB / ID: 7cbd
TitleCatalytic domain of Cellulomonas fimi Cel6B
ComponentsExoglucanase A
KeywordsHYDROLASE / Cellulase
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / cellulose catabolic process
Similarity search - Function
Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / Cellulose binding domain / Carbohydrate-binding type-2 domain ...Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsNakamura, A. / Ishiwata, D. / Visootsat, A. / Uchiyama, T. / Mizutani, K. / Kaneko, S. / Murata, T. / Igarashi, K. / Iino, R.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases.
Authors: Nakamura, A. / Ishiwata, D. / Visootsat, A. / Uchiyama, T. / Mizutani, K. / Kaneko, S. / Murata, T. / Igarashi, K. / Iino, R.
History
DepositionJun 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exoglucanase A


Theoretical massNumber of molelcules
Total (without water)49,1621
Polymers49,1621
Non-polymers00
Water16,105894
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.667, 49.390, 71.004
Angle α, β, γ (deg.)90.000, 96.360, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1157-

HOH

21A-1210-

HOH

31A-1322-

HOH

41A-1378-

HOH

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Components

#1: Protein Exoglucanase A / 1 / 4-beta-cellobiohydrolase A / CBP95 / Exocellobiohydrolase A


Mass: 49162.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (strain ATCC 484 / DSM 20113 / JCM 1341 / NBRC 15513 / NCIMB 8980 / NCTC 7547) (bacteria)
Strain: ATCC 484 / DSM 20113 / JCM 1341 / NBRC 15513 / NCIMB 8980 / NCTC 7547
Gene: cbhA, Celf_1925 / Production host: Escherichia coli (E. coli)
References: UniProt: P50401, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 894 / 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: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 5
Details: 21% PET3350, 10 mM sodium chloride, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 81834 / % possible obs: 89.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 8.12 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 39.2
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 10.9 / Num. unique obs: 3965 / % possible all: 87.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AVo

4avo


Resolution: 1.3→28.38 Å / SU ML: 0.0779 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.7352 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1559 2000 2.44 %
Rwork0.1256 79834 -
obs0.1263 81834 89.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.77 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 0 894 4242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563627
X-RAY DIFFRACTIONf_angle_d0.86265003
X-RAY DIFFRACTIONf_chiral_restr0.0906543
X-RAY DIFFRACTIONf_plane_restr0.006683
X-RAY DIFFRACTIONf_dihedral_angle_d10.92031994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.1781340.12355363X-RAY DIFFRACTION83.86
1.33-1.370.18131390.11915557X-RAY DIFFRACTION87.63
1.37-1.410.17131390.12095558X-RAY DIFFRACTION87.62
1.41-1.450.18821410.1185590X-RAY DIFFRACTION88.02
1.45-1.50.16791400.11425606X-RAY DIFFRACTION88.47
1.5-1.560.14651420.11125650X-RAY DIFFRACTION88.62
1.56-1.640.13881430.1115675X-RAY DIFFRACTION89.34
1.64-1.720.16781420.12145694X-RAY DIFFRACTION89.37
1.72-1.830.15411440.1265782X-RAY DIFFRACTION90.09
1.83-1.970.1471450.12945762X-RAY DIFFRACTION90.28
1.97-2.170.15131450.12515806X-RAY DIFFRACTION91.33
2.17-2.480.15221480.12955900X-RAY DIFFRACTION91.61
2.48-3.130.17421490.13845927X-RAY DIFFRACTION92.05
3.13-28.380.13781490.12615964X-RAY DIFFRACTION91.05

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