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- PDB-6k0v: Catalytic domain of GH87 alpha-1,3-glucanase D1069A in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6k0v
TitleCatalytic domain of GH87 alpha-1,3-glucanase D1069A 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
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 / Alpha-1,3-glucanase
Similarity search - Component
Biological speciesPaenibacillus glycanilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.504 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 / 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_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_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
B: Alpha-1,3-glucanase
C: Alpha-1,3-glucanase
D: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,47938
Polymers247,7404
Non-polymers5,73934
Water10,827601
1
A: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,56010
Polymers61,9351
Non-polymers1,6259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4649
Polymers61,9351
Non-polymers1,5298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,39810
Polymers61,9351
Non-polymers1,4639
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0569
Polymers61,9351
Non-polymers1,1218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.865, 132.617, 131.773
Angle α, β, γ (deg.)90.000, 90.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alpha-1,3-glucanase


Mass: 61935.047 Da / Num. of mol.: 4 / Fragment: Catalytic domain / Mutation: D1069A
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 , 3 types, 7 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.: 5
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)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose / alpha-nigerose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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 , 3 types, 628 molecules

#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.68 Å3/Da / Density % sol: 54.02 %
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, 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: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.504→46.905 Å / Num. obs: 88523 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.3
Reflection shellResolution: 2.504→2.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4522 / % possible all: 98.8

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Processing

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

6k0m


Resolution: 2.504→46.905 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.99
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2245 4408 4.98 %
Rwork0.1788 --
obs0.1811 88467 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.8 Å2 / Biso mean: 35.9061 Å2 / Biso min: 13.93 Å2
Refinement stepCycle: final / Resolution: 2.504→46.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17188 0 346 601 18135
Biso mean--55.35 35.92 -
Num. residues----2248
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 (%)
2.5043-2.53280.35061360.29832814295098
2.5328-2.56260.32891590.253227582917100
2.5626-2.59380.31081700.246228443014100
2.5938-2.62660.27531650.22728122977100
2.6266-2.66120.32841400.232628182958100
2.6612-2.69770.29171350.225228602995100
2.6977-2.73620.29341280.22128462974100
2.7362-2.7770.29391170.21828532970100
2.777-2.82040.29641560.210628322988100
2.8204-2.86660.26171640.205527612925100
2.8666-2.91610.27041510.203728693020100
2.9161-2.96910.28231590.213727902949100
2.9691-3.02620.28011570.208628583015100
3.0262-3.08790.29351530.212627932946100
3.0879-3.15510.27251570.205928603017100
3.1551-3.22850.25271370.196428042941100
3.2285-3.30920.21841270.185628502977100
3.3092-3.39860.26181530.17972820297399
3.3986-3.49860.21361680.17042766293499
3.4986-3.61150.22641260.16312866299299
3.6115-3.74050.20051000.15852832293299
3.7405-3.89020.18141590.15372764292398
3.8902-4.06720.18891950.14492709290497
4.0672-4.28140.18821680.13962720288897
4.2814-4.54950.18441320.13262709284195
4.5495-4.90040.16351480.12622690283894
4.9004-5.39290.17591320.14022752288496
5.3929-6.17180.18831470.17142758290597
6.1718-7.77010.21041000.18852883298398
7.7701-46.91280.18191690.19322768293796

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