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- PDB-3pzu: P212121 crystal form of the endo-1,4-beta-glucanase from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 3pzu
TitleP212121 crystal form of the endo-1,4-beta-glucanase from Bacillus subtilis 168
ComponentsEndoglucanase
KeywordsHYDROLASE / alpha/beta barrel / glycosyl hydrolase / cellulose binding
Function / homology
Function and homology information


glucan catabolic process / cellulose binding / cellulase / beta-glucosidase activity / cellulase activity / cellulose catabolic process / cell surface / extracellular region
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) ...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) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSantos, C.R. / Paiva, J.H. / Akao, P.K. / Meza, A.N. / Silva, J.C. / Squina, F.M. / Ward, R.J. / Ruller, R. / Murakami, M.T.
CitationJournal: Biochem.J. / Year: 2012
Title: Dissecting structure-function-stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168.
Authors: Santos, C.R. / Paiva, J.H. / Sforca, M.L. / Neves, J.L. / Navarro, R.Z. / Cota, J. / Akao, P.K. / Hoffmam, Z.B. / Meza, A.N. / Smetana, J.H. / Nogueira, M.L. / Polikarpov, I. / Xavier-Neto, ...Authors: Santos, C.R. / Paiva, J.H. / Sforca, M.L. / Neves, J.L. / Navarro, R.Z. / Cota, J. / Akao, P.K. / Hoffmam, Z.B. / Meza, A.N. / Smetana, J.H. / Nogueira, M.L. / Polikarpov, I. / Xavier-Neto, J. / Squina, F.M. / Ward, R.J. / Ruller, R. / Zeri, A.C. / Murakami, M.T.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Nov 15, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5735
Polymers72,2962
Non-polymers2763
Water5,945330
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2402
Polymers36,1481
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3323
Polymers36,1481
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.242, 110.762, 121.379
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 Endoglucanase / Carboxymethyl-cellulase / CMCase / Cellulase / Endo-1 / 4-beta-glucanase


Mass: 36148.203 Da / Num. of mol.: 2 / Fragment: catalytic domain, Unp residues 27-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: eglS, bglC, gld, BSU18130 / Production host: Escherichia coli (E. coli) / References: UniProt: P10475, cellulase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG1500, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.1→38.7 Å / Num. all: 72930 / Num. obs: 39069 / % possible obs: 97.2 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 85.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.298 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22081 1952 5 %RANDOM
Rwork0.17063 ---
all0.179 36885 --
obs0.17314 36885 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.69 Å2
Baniso -1Baniso -2Baniso -3
1-3.92 Å20 Å20 Å2
2---3.44 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4670 0 18 330 5018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224798
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.9316497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6225.391230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93315808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.11518
X-RAY DIFFRACTIONr_chiral_restr0.1520.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213662
X-RAY DIFFRACTIONr_mcbond_it1.0531.52933
X-RAY DIFFRACTIONr_mcangle_it1.77124695
X-RAY DIFFRACTIONr_scbond_it3.11731865
X-RAY DIFFRACTIONr_scangle_it4.7244.51802
LS refinement shellResolution: 2.103→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 129 -
Rwork0.202 2322 -
obs--84.58 %

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