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- PDB-5upn: Crystal structure of BhGH81 mutant in complex with laminaro-tetraose -

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Basic information

Entry
Database: PDB / ID: 5upn
TitleCrystal structure of BhGH81 mutant in complex with laminaro-tetraose
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 / Golgi alpha-mannosidase II; domain 4 / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Beta-galactosidase; Chain A, domain 5 / Galactose-binding-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-laminaribiose / beta-D-glucopyranose / alpha-D-glucopyranose / PHOSPHATE ION / Glucan endo-1,3-beta-D-glucosidase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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
DepositionFeb 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_comp_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
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: BH0236 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,45823
Polymers85,2781
Non-polymers3,18122
Water14,556808
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint5 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.610, 95.390, 158.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BH0236 protein


Mass: 85277.633 Da / Num. of mol.: 1 / Fragment: residues 28-779 / Mutation: E542Q
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

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Sugars , 4 types, 6 molecules

#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
#3: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / 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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 824 molecules

#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 10000, 0.2 M ammonium acetate, 0.1 M bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97971 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97971 Å / Relative weight: 1
ReflectionResolution: 1.8→79.14 Å / Num. obs: 89565 / % possible obs: 96.7 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.036 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 5.6 / CC1/2: 0.949 / Rpim(I) all: 0.116 / % possible all: 91.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T49

5t49


Resolution: 1.8→79.14 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.911 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.167 4412 4.9 %RANDOM
Rwork0.1487 ---
obs0.1496 85074 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 60.96 Å2 / Biso mean: 16.5 Å2 / Biso min: 2.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2--1.33 Å20 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.8→79.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 197 808 7026
Biso mean--25.38 29.83 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196553
X-RAY DIFFRACTIONr_bond_other_d0.0020.025724
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9428959
X-RAY DIFFRACTIONr_angle_other_deg0.884313163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2665787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9724.269342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37915940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1591531
X-RAY DIFFRACTIONr_chiral_restr0.0740.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021635
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 311 -
Rwork0.21 5818 -
all-6129 -
obs--90.79 %

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