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- PDB-5a8o: Crystal structure of beta-glucanase SdGluc5_26A from Saccharophag... -

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Basic information

Entry
Database: PDB / ID: 5a8o
TitleCrystal structure of beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with cellotetraose
ComponentsPUTATIVE RETAINING B-GLYCOSIDASE
KeywordsHYDROLASE / CAZYME / GLYCOSIDE HYDROLASE / BETA-GLUCANASE / GH5_26
Function / homology
Function and homology information


glucan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellotetraose / TRIETHYLENE GLYCOL / Putative retaining b-glycosidase
Similarity search - Component
Biological speciesSACCHAROPHAGUS DEGRADANS 2-40 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSulzenbacher, G. / Lafond, M. / Freyd, T. / Henrissat, B. / Coutinho, R.M. / Berrin, J.G. / Garron, M.L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Quaternary Structure of a Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans
Authors: Lafond, M. / Sulzenbacher, G. / Freyd, T. / Henrissat, B. / Berrin, J.G. / Garron, M.L.
History
DepositionJul 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_conn_angle / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,19115
Polymers42,0961
Non-polymers2,09614
Water5,242291
1
A: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules

A: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules

A: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,57445
Polymers126,2873
Non-polymers6,28742
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area15580 Å2
ΔGint-143.4 kcal/mol
Surface area38350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.773, 143.773, 143.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-2073-

HOH

21A-2143-

HOH

31A-2289-

HOH

41A-2290-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein PUTATIVE RETAINING B-GLYCOSIDASE / SDGLUC5_26A


Mass: 42095.680 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROPHAGUS DEGRADANS 2-40 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q21KE5, licheninase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 304 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 3.11 Å3/Da / Density % sol: 60.5 % / Description: NONE
Crystal growpH: 6
Details: 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM CACODYLATE BUFFER PH 6.0, 25% (W/V) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856
DetectorType: DECTRIS P / Date: May 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.3→47.92 Å / Num. obs: 23212 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A8N

5a8n


Resolution: 2.3→45.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.055 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.17282 1171 5.1 %RANDOM
Rwork0.14946 ---
obs0.15067 21999 99.88 %-
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: 26.595 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 99 291 3165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022992
X-RAY DIFFRACTIONr_bond_other_d0.0010.022743
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9544076
X-RAY DIFFRACTIONr_angle_other_deg0.74936346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26824.375144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5215471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3471512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02711
X-RAY DIFFRACTIONr_nbd_refined0.2380.2857
X-RAY DIFFRACTIONr_nbd_other0.170.22538
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21438
X-RAY DIFFRACTIONr_nbtor_other0.0810.21517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1760.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.150.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 88 -
Rwork0.194 1603 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 19.0402 Å / Origin y: 54.8978 Å / Origin z: 45.1988 Å
111213212223313233
T0.0263 Å20.0113 Å20.0075 Å2-0.0069 Å20.0033 Å2--0.0084 Å2
L0.4199 °2-0.0054 °2-0.1524 °2-0.2451 °2-0.1349 °2--0.3366 °2
S0.0258 Å °0.0014 Å °0.0369 Å °0.0461 Å °0.0198 Å °0.0138 Å °-0.0486 Å °-0.033 Å °-0.0456 Å °

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