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- PDB-2c3v: Structure of iodinated CBM25 from Bacillus halodurans amylase -

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Basic information

Entry
Database: PDB / ID: 2c3v
TitleStructure of iodinated CBM25 from Bacillus halodurans amylase
Components(ALPHA-AMYLASE G-6) x 2
KeywordsCARBOHYDRATE-BINDING MODULE / STARCH BINDING / CARBOHYDRATE BINDING / GLYCOSIDE HYDROLASE / AMYLOSE / AMYLOPECTIN / MALTO-OLIGOSACCHARIDE / CARBOHYDRATE- BINDING MODULE
Function / homology
Function and homology information


starch binding / carbohydrate metabolic process
Similarity search - Function
Carbohydrate binding module family 25 / Carbohydrate binding domain (family 25) / Carbohydrate binding domain / Starch-binding module 26 / Starch-binding module 26 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily / Immunoglobulins ...Carbohydrate binding module family 25 / Carbohydrate binding domain (family 25) / Carbohydrate binding domain / Starch-binding module 26 / Starch-binding module 26 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Alpha-amylase G-6
Similarity search - Component
Biological speciesBACILLUS HALODURANS (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.39 Å
AuthorsBoraston, A.B. / Healey, M. / Klassen, J. / Ficko-Blean, E. / Lammerts van Bueren, A. / Law, V.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: A Structural and Functional Analysis of Alpha-Glucan Recognition by Family 25 and 26 Carbohydrate-Binding Modules Reveals a Conserved Mode of Starch Recognition
Authors: Boraston, A.B. / Healey, M. / Klassen, J. / Ficko-Blean, E. / Lammerts Van Bueren, A. / Law, V.
History
DepositionOct 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-AMYLASE G-6
B: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1705
Polymers22,7902
Non-polymers3813
Water3,819212
1
A: ALPHA-AMYLASE G-6


Theoretical massNumber of molelcules
Total (without water)11,6471
Polymers11,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5244
Polymers11,1431
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.198, 41.819, 68.183
Angle α, β, γ (deg.)90.00, 97.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALPHA-AMYLASE G-6 / FAMILY 25 CARBOHYDRATE-BINDING MODULE


Mass: 11646.648 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 863-958
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS HALODURANS (bacteria) / Strain: C-125 / Plasmid: PET-BHCBM6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KFR4
#2: Protein ALPHA-AMYLASE G-6 / FAMILY 25 CARBOHYDRATE-BINDING MODULE


Mass: 11143.063 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 863-958
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS HALODURANS (bacteria) / Strain: C-125 / Plasmid: PET-BHCBM6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KFR4
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.13 %

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.39→20 Å / Num. obs: 28505 / % possible obs: 88 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.3

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.39→67.42 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.607 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1542 5.1 %RANDOM
Rwork0.201 ---
obs0.204 28505 88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.33 Å2
2--0.68 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.39→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 3 212 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211519
X-RAY DIFFRACTIONr_bond_other_d0.0030.021251
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.9352078
X-RAY DIFFRACTIONr_angle_other_deg0.98132923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4395190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1240.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021734
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02316
X-RAY DIFFRACTIONr_nbd_refined0.250.2288
X-RAY DIFFRACTIONr_nbd_other0.2680.21482
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.2892
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7151.5931
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.76221492
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3653588
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1954.5583
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: 1.39→1.43 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.418 56
Rwork0.519 1149

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