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- PDB-2c3h: Structure of CBM26 from Bacillus halodurans amylase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2c3h
TitleStructure of CBM26 from Bacillus halodurans amylase in complex with maltose
ComponentsALPHA-AMYLASE G-6
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
alpha-maltose / alpha-D-glucopyranose / Alpha-amylase G-6
Similarity search - Component
Biological speciesBACILLUS HALODURANS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.24 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 7, 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
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
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

Downloads & links

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Assembly

Deposited unit
A: ALPHA-AMYLASE G-6
B: ALPHA-AMYLASE G-6
C: ALPHA-AMYLASE G-6
D: ALPHA-AMYLASE G-6
E: ALPHA-AMYLASE G-6
F: ALPHA-AMYLASE G-6
G: ALPHA-AMYLASE G-6
H: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,49026
Polymers91,7078
Non-polymers3,78318
Water14,484804
1
A: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1906
Polymers11,4631
Non-polymers7275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8062
Polymers11,4631
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9984
Polymers11,4631
Non-polymers5343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9863
Polymers11,4631
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8062
Polymers11,4631
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9023
Polymers11,4631
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9984
Polymers11,4631
Non-polymers5343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: ALPHA-AMYLASE G-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8062
Polymers11,4631
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)108.204, 108.204, 180.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
ALPHA-AMYLASE G-6 / FAMILY 26 CARBOHYDRATE-BINDING MODULE


Mass: 11463.400 Da / Num. of mol.: 8 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 771-863
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: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 3 Å3/Da / Density % sol: 58.67 %

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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: 2.24→20 Å / Num. obs: 55701 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 2

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.24→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.129 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2964 5.1 %RANDOM
Rwork0.203 ---
obs0.207 55701 98.6 %-
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: 38.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20.57 Å20 Å2
2--1.14 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.24→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6219 0 241 804 7264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0216736
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.9429235
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9995729
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_restr0.1710.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025396
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.23535
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2737
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.53667
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6725937
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.52133069
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8374.53298
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: 2.24→2.29 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.359 182
Rwork0.29 3482

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