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- PDB-1w9s: Structure of a beta-1,3-glucan binding CBM6 from Bacillus halodurans -

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Basic information

Entry
Database: PDB / ID: 1w9s
TitleStructure of a beta-1,3-glucan binding CBM6 from Bacillus halodurans
ComponentsBH0236 PROTEIN
KeywordsCARBOHYDRATE-BINDING MODULE / LECTIN / BETA-GLUCAN / CARBOHYDRATE BINDING / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


endo-1,3(4)-beta-glucanase activity / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / polysaccharide catabolic process / cell wall organization / carbohydrate binding / extracellular region
Similarity search - Function
Glycosyl hydrolase family 81, N-terminal / Glycosyl hydrolase family 81 N-terminal domain / Endo-1,3(4)-beta-glucanase / Glycosyl hydrolase family 81, C-terminal domain / Glycosyl hydrolase family 81 C-terminal domain / Glycosyl hydrolases family 81 (GH81) domain profile. / : / Carbohydrate binding module family 56 / CBM56 (carbohydrate binding type-56) domain profile. / Cellulose binding, type IV ...Glycosyl hydrolase family 81, N-terminal / Glycosyl hydrolase family 81 N-terminal domain / Endo-1,3(4)-beta-glucanase / Glycosyl hydrolase family 81, C-terminal domain / Glycosyl hydrolase family 81 C-terminal domain / Glycosyl hydrolases family 81 (GH81) domain profile. / : / Carbohydrate binding module family 56 / CBM56 (carbohydrate binding type-56) domain profile. / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glucan endo-1,3-beta-D-glucosidase
Similarity search - Component
Biological speciesBACILLUS HALODURANS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBoraston, A.B. / van Bueren, A.L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Family 6 Carbohydrate Binding Modules Recognize the Non-Reducing End of Beta-1,3-Linked Glucans by Presenting a Unique Ligand Binding Surface
Authors: Van Bueren, A.L. / Moreland, C. / Gilbert, H.J. / Boraston, A.B.
History
DepositionOct 18, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BH0236 PROTEIN
B: BH0236 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,67010
Polymers31,3482
Non-polymers3228
Water6,305350
1
A: BH0236 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8355
Polymers15,6741
Non-polymers1614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BH0236 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8355
Polymers15,6741
Non-polymers1614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.795, 40.834, 56.118
Angle α, β, γ (deg.)108.95, 105.93, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein BH0236 PROTEIN / BHCBM6


Mass: 15673.985 Da / Num. of mol.: 2 / Fragment: CBM, RESIDUES 790-925
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS HALODURANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KG76
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.04 Å3/Da / Density % sol: 39.63 %

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→20 Å / Num. obs: 28471 / % possible obs: 90.1 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 24.9
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.7 / % possible all: 68.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GMM

1gmm


Resolution: 1.59→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.93 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.166 1517 5.1 %RANDOM
Rwork0.117 ---
obs0.119 28471 90.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å2-0.03 Å2-0.15 Å2
2---0.37 Å2-0.03 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 18 350 2476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212194
X-RAY DIFFRACTIONr_bond_other_d0.0010.021863
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9092987
X-RAY DIFFRACTIONr_angle_other_deg0.82634336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9095266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43124.959123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45415331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7791515
X-RAY DIFFRACTIONr_chiral_restr0.1250.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
X-RAY DIFFRACTIONr_nbd_refined0.2340.2397
X-RAY DIFFRACTIONr_nbd_other0.190.21983
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21085
X-RAY DIFFRACTIONr_nbtor_other0.0850.21293
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3750.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6711.51320
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.41622132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5463929
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1454.5855
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: 1.59→1.63 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 72
Rwork0.164 1415

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