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- PDB-7c7d: Crystal structure of the catalytic unit of thermostable GH87 alph... -

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Basic information

Entry
Database: PDB / ID: 7c7d
TitleCrystal structure of the catalytic unit of thermostable GH87 alpha-1,3-glucanase from Streptomyces thermodiastaticus strain HF3-3
Componentsalpha-1,3-glucanase
KeywordsHYDROLASE / glycosidase
Function / homology
Function and homology information


CBM6/CBM35/CBM36-like 1 / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / 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 ...CBM6/CBM35/CBM36-like 1 / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Biological speciesStreptomyces thermodiastaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.16 Å
AuthorsItoh, T. / Panti, N. / Toyotake, Y. / Hayashi, J. / Suyotha, W. / Yano, S. / Wakayama, M. / Hibi, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the catalytic unit of thermostable GH87 alpha-1,3-glucanase from Streptomyces thermodiastaticus strain HF3-3.
Authors: Itoh, T. / Panti, N. / Hayashi, J. / Toyotake, Y. / Matsui, D. / Yano, S. / Wakayama, M. / Hibi, T.
History
DepositionMay 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8715
Polymers126,5522
Non-polymers3183
Water19,6181089
1
A: alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3162
Polymers63,2761
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area18220 Å2
MethodPISA
2
B: alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5543
Polymers63,2761
Non-polymers2782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.508, 91.329, 164.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein alpha-1,3-glucanase


Mass: 63276.133 Da / Num. of mol.: 2 / Fragment: catalytic unit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces thermodiastaticus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G1KW31*PLUS, EC: 3.2.1.59
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1089 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.85 Å3/Da / Density % sol: 33.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 25% (w/v) polyethylene glycol 1500, 0.1 M malonate-imidazole-boric acid buffer, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→47 Å / Num. obs: 325339 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 11.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.7
Reflection shellResolution: 1.16→1.18 Å / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 15825 / CC1/2: 0.59

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZRU

5zru


Resolution: 1.16→41.21 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 14.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1586 16329 5.02 %
Rwork0.1349 308998 -
obs0.136 325327 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.93 Å2 / Biso mean: 20.9159 Å2 / Biso min: 8.17 Å2
Refinement stepCycle: final / Resolution: 1.16→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7934 0 18 1089 9041
Biso mean--44.46 38.41 -
Num. residues----1078
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 (%)
1.16-1.170.28935140.2495100301054498
1.17-1.180.27855810.24391022210803100
1.18-1.20.24725110.22991027810789100
1.2-1.210.23275400.21151019110731100
1.21-1.230.22185690.20051026310832100
1.23-1.250.2125670.18731018210749100
1.25-1.260.19875560.17761018010736100
1.26-1.280.19455690.17311026710836100
1.28-1.30.19425180.16191029910817100
1.3-1.320.18675000.16231026510765100
1.32-1.350.18775050.15471026110766100
1.35-1.370.16685130.14571029810811100
1.37-1.40.18045770.14281024010817100
1.4-1.430.16125330.1321028510818100
1.43-1.460.16475940.12231025810852100
1.46-1.490.14525320.11641026710799100
1.49-1.530.13385600.10931025510815100
1.53-1.570.1375630.10591025310816100
1.57-1.620.13675720.1071024310815100
1.62-1.670.13725390.10961033110870100
1.67-1.730.14725610.11531030910870100
1.73-1.80.15315330.11921033310866100
1.8-1.880.13755680.11761029710865100
1.88-1.980.1425120.11811037510887100
1.98-2.10.13855270.11781035110878100
2.1-2.260.14055300.1214103801091099
2.26-2.490.13835460.1314103751092199
2.49-2.850.15455370.1375104441098199
2.85-3.590.1595350.1351104871102299
3.59-41.210.16695670.1401107791134699

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