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- PDB-6ufw: Crystal structure of the CBM3 from Bacillus subtilis at 1.28 angs... -

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Basic information

Entry
Database: PDB / ID: 6ufw
TitleCrystal structure of the CBM3 from Bacillus subtilis at 1.28 angstrom resolution
ComponentsEndoglucanase
KeywordsHYDROLASE / Carbohydrate-binding module
Function / homology
Function and homology information


glucan exo-1,3-beta-glucosidase activity / glucan catabolic process / cellulose binding / cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å
AuthorsMorais, M.A.B. / Paiva, J.H. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)08/10555-1 Brazil
CitationJournal: To Be Published
Title: Crystal structure of the CBM3 from Bacillus subtilis at 1.28 angstrom resolution
Authors: Morais, M.A.B. / Paiva, J.H. / Murakami, M.T.
History
DepositionSep 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)16,7181
Polymers16,7181
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.092, 55.176, 89.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

21A-653-

HOH

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Components

#1: Protein Endoglucanase / Carboxymethyl-cellulase / Cellulase / Endo-1 / 4-beta-glucanase


Mass: 16717.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: eglS, bglC, gld, BSU18130 / Production host: Escherichia coli (E. coli) / References: UniProt: P10475, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20 % (w/v) PEG3350, 0.20 M potassium thiocynate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.28→28.727 Å / Num. obs: 31335 / % possible obs: 95.07 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.76 Å2 / CC1/2: 0.99 / Net I/σ(I): 28.27
Reflection shellResolution: 1.28→1.325 Å / Num. unique obs: 2914 / CC1/2: 0.99
Serial crystallography sample deliveryMethod: fixed target

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→28.727 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.59
RfactorNum. reflection% reflection
Rfree0.1731 1635 5.22 %
Rwork0.1463 --
obs0.1478 31333 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 44.72 Å2 / Biso mean: 16.69 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 1.28→28.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 0 216 1394
Biso mean---26.59 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011237
X-RAY DIFFRACTIONf_angle_d1.3041678
X-RAY DIFFRACTIONf_chiral_restr0.053176
X-RAY DIFFRACTIONf_plane_restr0.007222
X-RAY DIFFRACTIONf_dihedral_angle_d12.906451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.28-1.31740.21571150.1447230389
1.3174-1.35990.18441310.1325235292
1.3599-1.40850.1751520.1251238893
1.4085-1.46490.18371360.123243094
1.4649-1.53160.19661130.1294244595
1.5316-1.61230.18311280.1312248696
1.6123-1.71330.18061440.1323248696
1.7133-1.84560.18191290.1357249896
1.8456-2.03130.16461420.1388253497
2.0313-2.32510.16091620.141254098
2.3251-2.92890.19931350.1632260298

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