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- PDB-4azz: Carbohydrate binding module CBM66 from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 4azz
TitleCarbohydrate binding module CBM66 from Bacillus subtilis
ComponentsLEVANASE
KeywordsHYDROLASE / LEVAN
Function / homology
Function and homology information


fructan beta-fructosidase / fructan beta-fructosidase activity / sucrose alpha-glucosidase activity / sucrose catabolic process / extracellular region / cytoplasm
Similarity search - Function
3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain ...3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsGloster, T.M. / Flint, J.E. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: How Nature Can Exploit Nonspecific Catalytic and Carbohydrate Binding Modules to Create Enzymatic Specificity.
Authors: Cuskin, F. / Flint, J.E. / Gloster, T.M. / Morland, C. / Basle, A. / Henrissat, B. / Coutinho, P.M. / Strazzulli, A. / Solovyova, A.S. / Davies, G.J. / Gilbert, H.J.
History
DepositionJun 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEVANASE
B: LEVANASE


Theoretical massNumber of molelcules
Total (without water)38,3622
Polymers38,3622
Non-polymers00
Water6,269348
1
A: LEVANASE


Theoretical massNumber of molelcules
Total (without water)19,1811
Polymers19,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LEVANASE


Theoretical massNumber of molelcules
Total (without water)19,1811
Polymers19,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.837, 60.950, 71.121
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LEVANASE / / BETA-D-FRUCTOFURANOSIDASE / EXO-BETA-D-FRUCTOSIDASE / EXO-LEVANASE


Mass: 19181.127 Da / Num. of mol.: 2 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 515-677
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05656, fructan beta-fructosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCARBOHYDRATE BINDING MODULE WAS PREDICTED TO COMPRISE RESIDUES 515-677 OF THE FULL LENGTH PROTEIN. ...CARBOHYDRATE BINDING MODULE WAS PREDICTED TO COMPRISE RESIDUES 515-677 OF THE FULL LENGTH PROTEIN. N-TERMINAL METHIONINE AND C-TERMINAL HIS TAG (LEHHHHHH) WERE ADDED FOR EXPRESSION AND PURIFICATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.3 %
Description: PHASING WAS DONE FROM A DIFFERENT DATA SET WITH SEMET INCORPORATION - ADDITIONAL INFORMATION PROVIDED BELOW. THE NATIVE HIGHER RESOLUTION DATA WERE USED FOR REFINEMENT FOLLOWING STRUCTURE SOLUTION.
Crystal growDetails: PROTEIN AT 20 MG/ML FROM 1 M LICL, 20% POLYETHYLENE 6000 AND 0.1 M CITRIC ACID, PH 4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-210.933
SYNCHROTRONESRF ID23-120.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 16, 2006
ADSC QUANTUM 315r2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.9791
ReflectionResolution: 1.7→30 Å / Num. obs: 32834 / % possible obs: 98.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→69.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.142 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20628 1668 5.1 %RANDOM
Rwork0.15734 ---
obs0.15986 31147 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20.31 Å2
2---0.06 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.7→69.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 0 348 2922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9333979
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4185417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29824.792144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75915525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2181514
X-RAY DIFFRACTIONr_chiral_restr0.1240.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022262
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.696→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 110 -
Rwork0.246 2130 -
obs--93.65 %

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