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- PDB-5t49: Crystal structure of SeMet derivative BhGH81 -

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Basic information

Entry
Database: PDB / ID: 5t49
TitleCrystal structure of SeMet derivative BhGH81
ComponentsBH0236 protein
KeywordsHYDROLASE / (alpha/beta)6 barrel / 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-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Glucan endo-1,3-beta-D-glucosidase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.5 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Structure / Year: 2017
Title: Structural Analysis of a Family 81 Glycoside Hydrolase Implicates Its Recognition of beta-1,3-Glucan Quaternary Structure.
Authors: Pluvinage, B. / Fillo, A. / Massel, P. / Boraston, A.B.
History
DepositionAug 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author / pdbx_audit_support
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 / _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,85819
Polymers89,4441
Non-polymers1,41318
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-23 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.540, 94.290, 159.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BH0236 protein


Mass: 89444.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (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.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.2
Details: 1.4/0.35 M NaH2PO4/K2HPO4, 0.075 M Na2HPO4/citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97944 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: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.5→81.12 Å / Num. obs: 34789 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 1 / Rmerge(I) obs: 0.169 / Net I/σ(I): 14.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 7.3 / CC1/2: 0.92 / % possible all: 99.9

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Phasing

Phasing
Method
SAD
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: SAD / Resolution: 2.5→81.12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.97 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.212
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 1745 5 %RANDOM
Rwork0.1417 ---
obs0.1441 33043 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.49 Å2 / Biso mean: 14.577 Å2 / Biso min: 2.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--1.25 Å20 Å2
3----0.86 Å2
Refinement stepCycle: final / Resolution: 2.5→81.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6020 0 81 337 6438
Biso mean--35.7 15.92 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196301
X-RAY DIFFRACTIONr_bond_other_d0.0020.025524
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9298579
X-RAY DIFFRACTIONr_angle_other_deg0.931312678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7265.013758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32124.196336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49515864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0951530
X-RAY DIFFRACTIONr_chiral_restr0.0820.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021596
X-RAY DIFFRACTIONr_mcbond_it0.7581.4063022
X-RAY DIFFRACTIONr_mcbond_other0.7571.4053021
X-RAY DIFFRACTIONr_mcangle_it1.3222.1053781
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 120 -
Rwork0.171 2403 -
all-2523 -
obs--99.92 %

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