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- PDB-6k0m: Catalytic domain of GH87 alpha-1,3-glucanase from Paenibacillus g... -

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Basic information

Entry
Database: PDB / ID: 6k0m
TitleCatalytic domain of GH87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11
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 / SAD / Resolution: 1.6 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: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,33216
Polymers61,9791
Non-polymers1,35315
Water16,232901
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-67 kcal/mol
Surface area19350 Å2
Unit cell
Length a, b, c (Å)132.602, 132.602, 76.131
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-2657-

HOH

21A-2968-

HOH

31A-2992-

HOH

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Components

#1: Protein Alpha-1,3-glucanase


Mass: 61979.055 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus glycanilyticus (bacteria)
Gene: agl / Variant: FH11 / Production host: Brevibacillus CHOSHINENSIS (bacteria) / References: UniProt: A0A068PS59
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: counter-diffusion / 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: AichiSR / Beamline: BL2S1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→33.116 Å / Num. obs: 89574 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 27.8
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.723 / Num. unique obs: 4426

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→33.116 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.42
RfactorNum. reflection% reflection
Rfree0.1626 4457 4.98 %
Rwork0.142 --
obs0.1431 89481 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.6 Å2 / Biso mean: 14.9403 Å2 / Biso min: 4.17 Å2
Refinement stepCycle: final / Resolution: 1.6→33.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 0 79 901 5262
Biso mean--27.25 28.25 -
Num. residues----559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6001-1.61830.24651380.186128102948
1.6183-1.63730.19761220.184327732895
1.6373-1.65730.22351360.175228472983
1.6573-1.67830.24381400.168728042944
1.6783-1.70030.17961820.162727632945
1.7003-1.72360.18781650.160927752940
1.7236-1.74830.19761510.160227952946
1.7483-1.77440.18881410.150428072948
1.7744-1.80210.17791280.14828132941
1.8021-1.83160.17641590.152627832942
1.8316-1.86320.17131550.146128242979
1.8632-1.89710.17311450.144527922937
1.8971-1.93360.15861540.139827952949
1.9336-1.9730.16151650.136428052970
1.973-2.01590.13811650.13628162981
2.0159-2.06280.13221440.134628212965
2.0628-2.11440.17151560.13927992955
2.1144-2.17150.14841460.136728272973
2.1715-2.23540.17161390.133728172956
2.2354-2.30760.14241440.136928332977
2.3076-2.390.17441560.14228312987
2.39-2.48570.16461430.142628362979
2.4857-2.59880.1641380.145728683006
2.5988-2.73570.16571450.143428472992
2.7357-2.9070.16791490.142828492998
2.907-3.13130.18671210.141728973018
3.1313-3.44610.13621550.133228803035
3.4461-3.94410.12881540.122628993053
3.9441-4.96650.13981490.114829413090
4.9665-33.12270.17911720.174930773249

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