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- PDB-5t7a: Crystal structure of Br derivative BhCBM56 -

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Basic information

Entry
Database: PDB / ID: 5t7a
TitleCrystal structure of Br derivative BhCBM56
ComponentsBH0236 protein
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding module
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 / cell surface / extracellular region
Similarity search - Function
Glycosyl hydrolase family 81, N-terminal / Glycosyl hydrolase family 81 N-terminal domain / Glycosyl hydrolases family 81 (GH81) domain profile. / Endo-1,3(4)-beta-glucanase / Glycosyl hydrolase family 81, C-terminal domain / Glycosyl hydrolase family 81 C-terminal domain / : / CBM56 (carbohydrate binding type-56) domain profile. / Cellulose binding, type IV / Cellulose Binding Domain Type IV ...Glycosyl hydrolase family 81, N-terminal / Glycosyl hydrolase family 81 N-terminal domain / Glycosyl hydrolases family 81 (GH81) domain profile. / Endo-1,3(4)-beta-glucanase / Glycosyl hydrolase family 81, C-terminal domain / Glycosyl hydrolase family 81 C-terminal domain / : / 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-like domain superfamily
Similarity search - Domain/homology
BROMIDE ION / Glucan endo-1,3-beta-D-glucosidase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 1.6 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Properties of a family 56 carbohydrate-binding module and its role in the recognition and hydrolysis of beta-1,3-glucan.
Authors: Hettle, A. / Fillo, A. / Abe, K. / Massel, P. / Pluvinage, B. / Langelaan, D.N. / Smith, S.P. / Boraston, A.B.
History
DepositionSep 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)27,84916
Polymers26,8552
Non-polymers99414
Water5,224290
1
A: BH0236 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9959
Polymers13,4281
Non-polymers5688
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BH0236 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8547
Polymers13,4281
Non-polymers4266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.271, 54.258, 57.820
Angle α, β, γ (deg.)90.000, 130.860, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1206-

HOH

21B-1211-

HOH

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Components

#1: Protein BH0236 protein


Mass: 13427.587 Da / Num. of mol.: 2 / Fragment: Carbohydrate Binding Module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: BH0236 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KG76
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 1.68 Å3/Da / Density % sol: 26.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 21% PEG 3350, 0.1M BisTris/HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91966 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91966 Å / Relative weight: 1
ReflectionResolution: 1.6→43.73 Å / Num. obs: 23416 / % possible obs: 99.1 % / Redundancy: 13.7 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Net I/σ(I): 36.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 4.4 / CC1/2: 0.92 / % possible all: 99.5

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
SHARPphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.6→43.73 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.502 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.084
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1772 1231 5.3 %RANDOM
Rwork0.1464 ---
obs0.1481 22183 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.71 Å2 / Biso mean: 14.731 Å2 / Biso min: 6.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.6→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1511 0 35 290 1836
Biso mean--33.75 26.32 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191610
X-RAY DIFFRACTIONr_bond_other_d0.0030.021419
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9272184
X-RAY DIFFRACTIONr_angle_other_deg1.03433256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1345193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22923.63688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.56215243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6861512
X-RAY DIFFRACTIONr_chiral_restr0.1260.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021872
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02412
X-RAY DIFFRACTIONr_mcbond_it1.3611.27760
X-RAY DIFFRACTIONr_mcbond_other1.3571.269759
X-RAY DIFFRACTIONr_mcangle_it2.0291.901954
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 92 -
Rwork0.2 1617 -
all-1709 -
obs--99.36 %

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