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- PDB-7kw6: Crystal structure of the BlCel48B from Bacillus licheniformis -

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Basic information

Entry
Database: PDB / ID: 7kw6
TitleCrystal structure of the BlCel48B from Bacillus licheniformis
ComponentsExoglucanase-2
KeywordsHYDROLASE / Enzyme / GH48 / Cellulase / Processive
Function / homologybeta-cellobiose / beta-cellotetraose / :
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsAraujo, E.A. / Polikarpov, I.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15/13684-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)158752/2015-5 Brazil
CitationJournal: Carbohydr Polym / Year: 2021
Title: Impact of cellulose properties on enzymatic degradation by bacterial GH48 enzymes: Structural and mechanistic insights from processive Bacillus licheniformis Cel48B cellulase.
Authors: Araujo, E.A. / Dias, A.H.S. / Kadowaki, M.A.S. / Piyadov, V. / Pellegrini, V.O.A. / Urio, M.B. / Ramos, L.P. / Skaf, M.S. / Polikarpov, I.
History
DepositionNov 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exoglucanase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,38116
Polymers79,5871
Non-polymers1,79415
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.537, 98.980, 59.910
Angle α, β, γ (deg.)90.000, 103.136, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Exoglucanase-2 / Processive cellulase from glycoside hydrolase family 48


Mass: 79587.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: CHCC14429_0452 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A6I7VUD0

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


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
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 591 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 8.5
Details: 0.5M LiCl, 24-28% PEG 6000, 0.1 M Tris, 0.005 M CaCl2

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45859 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45859 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 146189 / % possible obs: 96.1 % / Redundancy: 3 % / Biso Wilson estimate: 12.88 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.076 / Net I/av σ(I): 2.4 / Net I/σ(I): 13.61
Reflection shellResolution: 1.68→5.02 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 75730 / CC1/2: 0.997 / CC star: 0.999 / Rrim(I) all: 0.0779 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BV9

5bv9


Resolution: 1.68→29.7 Å / SU ML: 0.1709 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 18.3151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1807 2000 2.64 %
Rwork0.1479 73800 -
obs0.1488 75800 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.85 Å2
Refinement stepCycle: LAST / Resolution: 1.68→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 117 578 6269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01575875
X-RAY DIFFRACTIONf_angle_d1.63238006
X-RAY DIFFRACTIONf_chiral_restr0.1106800
X-RAY DIFFRACTIONf_plane_restr0.01131035
X-RAY DIFFRACTIONf_dihedral_angle_d6.8837778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.3121350.23854931X-RAY DIFFRACTION92.29
1.72-1.770.23661370.21685054X-RAY DIFFRACTION94.35
1.77-1.820.23181480.18515221X-RAY DIFFRACTION98.8
1.82-1.880.20391450.16045293X-RAY DIFFRACTION99.41
1.88-1.950.1841410.14595299X-RAY DIFFRACTION99.31
1.95-2.020.18971470.1415297X-RAY DIFFRACTION99.23
2.02-2.120.18061410.13785280X-RAY DIFFRACTION98.92
2.12-2.230.20651440.14045336X-RAY DIFFRACTION99.56
2.23-2.370.16481390.13895300X-RAY DIFFRACTION99.38
2.37-2.550.18931440.14635327X-RAY DIFFRACTION99.51
2.55-2.810.17861440.14695307X-RAY DIFFRACTION99.47
2.81-3.210.1551480.14415338X-RAY DIFFRACTION99.44
3.21-4.040.16561420.13365363X-RAY DIFFRACTION99.82
4.05-5.020.15031450.14075454X-RAY DIFFRACTION99.8

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