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- PDB-6d2x: Crystal structure of the GH26 domain from PbGH26-GH5A endo-beta-m... -

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Basic information

Entry
Database: PDB / ID: 6d2x
TitleCrystal structure of the GH26 domain from PbGH26-GH5A endo-beta-mannanase/endo-beta-glucanase from Prevotella bryantii
ComponentsAryl-phospho-beta-D-glucosidase BglC, GH1 family
KeywordsHYDROLASE / glycosyl hydrolase family 26 / glycosyl hydrolase family 5 / GH26 / GH5 / mannanase / glucanase / polysaccharide utilization locus / Prevotella bryantii
Function / homology
Function and homology information


: / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-PE3 / Aryl-phospho-beta-D-glucosidase BglC, GH1 family
Similarity search - Component
Biological speciesPrevotella bryantii B14 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsStogios, P.J. / Skarina, T. / McGregor, N. / Di Leo, R. / Brumer, H. / Savchenko, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Industrial Biocatalysis Network Canada
CitationJournal: To Be Published
Title: Crystal structure of the GH26 domain from PbGH26-GH5A endo-beta-mannanase/endo-beta-glucanase from Prevotella bryantii
Authors: McGregor, N.
History
DepositionApr 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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: Aryl-phospho-beta-D-glucosidase BglC, GH1 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,70210
Polymers38,1481
Non-polymers3,5549
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-36 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.577, 73.577, 105.086
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-987-

HOH

21A-990-

HOH

31A-1020-

HOH

41A-1140-

HOH

51A-1146-

HOH

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Components

#1: Protein Aryl-phospho-beta-D-glucosidase BglC, GH1 family / B-1 / 4-endoglucanase


Mass: 38148.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella bryantii B14 (bacteria) / Gene: PBR_0368, SAMN05444375_1266 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: D8DY19
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C28H58O15
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 M ammonium sulfate, 2% (w/v) PEG200, 15 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. obs: 35561 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Net I/σ(I): 36.3
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.142 / Mean I/σ(I) obs: 2.14 / Num. unique all: 1761 / CC1/2: 0.607 / Rpim(I) all: 0.492 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D2W

6d2w


Resolution: 1.72→27.243 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 1782 5.02 %RANDOM
Rwork0.1526 ---
obs0.1547 35526 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→27.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 62 547 3297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012859
X-RAY DIFFRACTIONf_angle_d0.9923893
X-RAY DIFFRACTIONf_dihedral_angle_d16.413998
X-RAY DIFFRACTIONf_chiral_restr0.062392
X-RAY DIFFRACTIONf_plane_restr0.007496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7197-1.76620.31061340.26892520X-RAY DIFFRACTION99
1.7662-1.81820.25241340.23012570X-RAY DIFFRACTION100
1.8182-1.87690.26281370.22382582X-RAY DIFFRACTION100
1.8769-1.94390.26191360.20112568X-RAY DIFFRACTION100
1.9439-2.02170.23781330.16772541X-RAY DIFFRACTION100
2.0217-2.11370.20071360.16192588X-RAY DIFFRACTION100
2.1137-2.22510.18351330.16382585X-RAY DIFFRACTION100
2.2251-2.36440.21651360.15562591X-RAY DIFFRACTION100
2.3644-2.54690.21771380.16052587X-RAY DIFFRACTION100
2.5469-2.80290.19541390.15722591X-RAY DIFFRACTION100
2.8029-3.2080.1961410.14122631X-RAY DIFFRACTION100
3.208-4.03960.16271380.12492634X-RAY DIFFRACTION100
4.0396-27.24620.17321470.1372756X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8861-0.18410.82511.7141-0.00842.01660.03320.1308-0.0758-0.21710.0883-0.1685-0.00990.0978-0.10870.2057-0.01210.0210.1195-0.02230.1668-28.3673-10.6149-15.1194
23.5326-2.47973.2675.98690.98275.5650.0344-0.2213-0.43670.60420.11860.50240.5616-0.4971-0.0930.216-0.05460.0160.18680.02730.2038-27.4256-8.38287.0911
31.1391.02931.1043.68952.71523.2548-0.0288-0.0061-0.05080.03280.1839-0.2463-0.07340.2796-0.15730.167-0.00820.00720.18970.00550.1768-20.8914-0.29642.7329
40.92310.16860.50381.02970.02541.8917-0.06680.09690.127-0.10520.0481-0.1312-0.41620.17480.02040.2711-0.03240.04420.1889-0.00310.1981-23.53086.1832-15.1203
53.58810.4235-0.32632.3008-0.39113.75870.04980.0916-0.2015-0.21860.0471-0.00910.0932-0.1901-0.08020.2097-0.0147-0.02310.13920.01730.1525-37.9961-6.8137-18.7387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 92 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 248 )
4X-RAY DIFFRACTION4chain 'A' and (resid 249 through 389 )
5X-RAY DIFFRACTION5chain 'A' and (resid 390 through 427 )

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