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- PDB-6k0p: Catalytic domain of GH87 alpha-1,3-glucanase D1045A in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6k0p
TitleCatalytic domain of GH87 alpha-1,3-glucanase D1045A in complex with nigerose
ComponentsAlpha-1,3-glucanase
KeywordsHYDROLASE / GH87 alpha-1 / 3-glucanase / catalytic domain
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
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 ...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
alpha-nigerose / ACETIC ACID / Alpha-1,3-glucanase
Similarity search - Component
Biological speciesPaenibacillus glycanilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.424 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: 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _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)63,60212
Polymers61,9351
Non-polymers1,66711
Water15,817878
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 area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.525, 132.525, 76.147
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-2704-

HOH

21A-2710-

HOH

31A-2956-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein Alpha-1,3-glucanase


Mass: 61935.047 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Mutation: D1045A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus glycanilyticus (bacteria)
Gene: agl / Production host: Brevibacillus (bacteria) / References: UniProt: A0A068PS59
#2: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose / alpha-nigerose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-nigerose
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 886 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M (NH4)2SO4, 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: 1.42→46.855 Å / Num. obs: 125008 / % possible obs: 98.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 9.2
Reflection shellResolution: 1.42→1.51 Å / Rmerge(I) obs: 1.254 / Num. unique obs: 38213

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6k0m


Resolution: 1.424→36.756 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.76
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.1704 6162 4.93 %
Rwork0.1556 --
obs0.1563 125008 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.11 Å2 / Biso mean: 16.7823 Å2 / Biso min: 4.71 Å2
Refinement stepCycle: final / Resolution: 1.424→36.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 0 103 878 5260
Biso mean--24.09 29.22 -
Num. residues----559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4236-1.43970.27262030.25923729393294
1.4397-1.45670.2651930.25673877407098
1.4567-1.47440.24352020.25063872407498
1.4744-1.49310.26742010.2383881408298
1.4931-1.51270.24712190.24213861408098
1.5127-1.53350.25152110.22233890410198
1.5335-1.55540.24242180.21023870408898
1.5554-1.57860.21461800.19673937411799
1.5786-1.60330.22352080.1883907411599
1.6033-1.62950.20762170.18963897411498
1.6295-1.65760.22742100.18643916412698
1.6576-1.68780.20291620.17563935409799
1.6878-1.72020.18152060.16793940414699
1.7202-1.75540.17572020.16843943414599
1.7554-1.79350.19082030.16373923412699
1.7935-1.83520.19562100.16323945415599
1.8352-1.88110.16792140.14973917413199
1.8811-1.9320.16521830.1464006418999
1.932-1.98880.15181860.14093982416899
1.9888-2.0530.13862080.13643984419299
2.053-2.12640.15752320.13993950418299
2.1264-2.21150.15962060.136640014207100
2.2115-2.31220.13892100.137139964206100
2.3122-2.43410.15181970.146140364233100
2.4341-2.58650.18042040.146140254229100
2.5865-2.78620.16281930.153340534246100
2.7862-3.06640.16892520.150540334285100
3.0664-3.50980.13832070.136740824289100
3.5098-4.42080.13332110.121341444355100
4.4208-36.76810.1762140.16274314452899

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