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- PDB-5v1w: Crystal structure of BhGH81 in complex with laminaro-biose -

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Basic information

Entry
Database: PDB / ID: 5v1w
TitleCrystal structure of BhGH81 in complex with laminaro-biose
ComponentsGlycoside Hydrolase
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
beta-laminaribiose / PHOSPHATE ION / Glucan endo-1,3-beta-D-glucosidase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsPluvinage, B. / Boraston, A.B.
CitationJournal: Structure / Year: 2017
Title: The quaternary structure of beta-1,3-glucan contributes to its recognition and hydrolysis by a multimodular family 81 glycoside hydrolase
Authors: Pluvinage, B. / Fillo, A. / Massel, P. / Boraston, A.B.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,16720
Polymers85,1641
Non-polymers2,00319
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-6 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.547, 93.854, 159.204
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 Glycoside Hydrolase / BH0236 protein


Mass: 85163.539 Da / Num. of mol.: 1 / Fragment: residues 28-778
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: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 1.2 M NaH2PO4, 0.2 M K2HPO4, 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.15→80.85 Å / Num. obs: 54002 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.084 / Net I/σ(I): 7.8
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.708 / Rpim(I) all: 0.326 / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T4A

5t4a


Resolution: 2.15→80.85 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.841 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.185 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 2690 5 %RANDOM
Rwork0.1868 ---
obs0.189 50866 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.88 Å2 / Biso mean: 27.208 Å2 / Biso min: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 2.15→80.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6013 0 122 595 6730
Biso mean--36.01 35.19 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196336
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9278631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0624.239335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74815908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2291529
X-RAY DIFFRACTIONr_chiral_restr0.0840.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215001
LS refinement shellResolution: 2.148→2.204 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 203 -
Rwork0.227 3561 -
all-3764 -
obs--94.67 %

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