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- PDB-6k0u: Catalytic domain of GH87 alpha-1,3-glucanase D1068A in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6k0u
TitleCatalytic domain of GH87 alpha-1,3-glucanase D1068A in complex with tetrasaccharides
ComponentsAlpha-1,3-glucanase
KeywordsHYDROLASE / GH87 alpha-1 / 3-glucanase / catalytic domain
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
: / CBM6/CBM35/CBM36-like 1 / Alpha-1,3-glucanase catalytic domain D2 / Alpha-1,3-glucanase catalytic domain D1 / CARDB domain / CARDB / Carbohydrate binding module (family 35) / Parallel beta-helix repeat / Parallel beta-helix repeats / CBM6 (carbohydrate binding type-6) domain profile. ...: / CBM6/CBM35/CBM36-like 1 / Alpha-1,3-glucanase catalytic domain D2 / Alpha-1,3-glucanase catalytic domain D1 / CARDB domain / CARDB / Carbohydrate binding module (family 35) / Parallel beta-helix repeat / Parallel beta-helix repeats / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Pectin lyase fold / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Pectin lyase fold/virulence factor / Galactose-binding-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesPaenibacillus glycanilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsItoh, T. / Intuy, R. / Suyotha, W. / Hayashi, J. / Yano, S. / Makabe, K. / Wakayama, M. / Hibi, T.
CitationJournal: Febs J. / Year: 2020
Title: Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11.
Authors: Itoh, T. / Intuy, R. / Suyotha, W. / Hayashi, J. / Yano, S. / Makabe, K. / Wakayama, M. / Hibi, T.
History
DepositionMay 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
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 / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,72310
Polymers61,9351
Non-polymers1,7879
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.966, 132.966, 76.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2513-

HOH

21A-2635-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-1,3-glucanase


Mass: 61935.047 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Mutation: D1068A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus glycanilyticus (bacteria)
Gene: agl / Production host: Brevibacillus (bacteria) / References: UniProt: A0A068PS59

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-3DGlcpa1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 558 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M (NH4)2SO4 and 25% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→42.048 Å / Num. obs: 49682 / % possible obs: 99 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 8.9
Reflection shellResolution: 1.95→2.07 Å / Rmerge(I) obs: 1.277 / Num. unique obs: 15277

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K0M

6k0m


Resolution: 1.95→42.048 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.07
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2056 2491 5.01 %
Rwork0.1801 --
obs0.1814 49682 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93 Å2 / Biso mean: 30.3606 Å2 / Biso min: 14.96 Å2
Refinement stepCycle: final / Resolution: 1.95→42.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 0 110 551 4940
Biso mean--52.99 37.06 -
Num. residues----559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9499-1.98740.30111600.25882518267897
1.9874-2.0280.25291380.242126072745100
2.028-2.07210.27421280.228626562784100
2.0721-2.12030.27861390.226226072746100
2.1203-2.17330.25521230.21826242747100
2.1733-2.23210.35941270.2972356248389
2.2321-2.29770.47121150.40222310242588
2.2977-2.37190.2541380.211826422780100
2.3719-2.45670.21951280.191726472775100
2.4567-2.5550.23411270.191426682795100
2.555-2.67130.22591430.180826252768100
2.6713-2.81210.23451380.175626612799100
2.8121-2.98820.20641620.173126372799100
2.9882-3.21890.20651380.169726722810100
3.2189-3.54260.15841310.149826932824100
3.5426-4.05490.15731550.144226872842100
4.0549-5.10730.14081660.117627132879100
5.1073-42.05730.17391350.1682868300399

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