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- PDB-9bmk: GH5_4 endo-beta(1,3/1,4)-glucanase E331A from Segatella copri in ... -

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Basic information

Entry
Database: PDB / ID: 9bmk
TitleGH5_4 endo-beta(1,3/1,4)-glucanase E331A from Segatella copri in complex with cellotriose
ComponentsCellulase (Glycosyl hydrolase family 5)
KeywordsHYDROLASE / Segatella copri / mixed-linkage beta-glucan / MLG / GH5_4 / cellotriose
Function / homology
Function and homology information


beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-cellotriose / Cellulase (Glycosyl hydrolase family 5)
Similarity search - Component
Biological speciesSegatella copri DSM 18205 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsCordeiro, R.L. / Golisch, B. / Brumer, H. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The molecular basis of cereal mixed-linkage beta-glucan utilization by the human gut bacterium Segatella copri.
Authors: Golisch, B. / Cordeiro, R.L. / Fraser, A.S.C. / Briggs, J. / Stewart, W.A. / Van Petegem, F. / Brumer, H.
History
DepositionMay 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulase (Glycosyl hydrolase family 5)
B: Cellulase (Glycosyl hydrolase family 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7258
Polymers83,5152
Non-polymers2,2106
Water18010
1
A: Cellulase (Glycosyl hydrolase family 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8634
Polymers41,7581
Non-polymers1,1053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulase (Glycosyl hydrolase family 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8634
Polymers41,7581
Non-polymers1,1053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.550, 107.550, 232.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Cellulase (Glycosyl hydrolase family 5)


Mass: 41757.625 Da / Num. of mol.: 2 / Mutation: E331A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Segatella copri DSM 18205 (bacteria) / Gene: PREVCOP_05101 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D1PD14
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.64 Å3/Da / Density % sol: 73.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulfate, 0.1 M potassium sodium tartrate tetrahydrate
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.21→48.84 Å / Num. obs: 149544 / % possible obs: 99.54 % / Redundancy: 1.9 % / Biso Wilson estimate: 57.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02363 / Net I/σ(I): 14.14
Reflection shellResolution: 2.21→2.289 Å / Rmerge(I) obs: 0.9453 / Num. unique obs: 7730 / CC1/2: 0.674

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Processing

Software
NameVersionClassification
PDB-REDOrefinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→48.8 Å / SU ML: 0.3904 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.8057
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 3783 2.53 %RANDOM
Rwork0.2216 145761 --
obs0.2221 149544 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.26 Å2
Refinement stepCycle: LAST / Resolution: 2.21→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5894 0 146 10 6050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00866208
X-RAY DIFFRACTIONf_angle_d0.97938432
X-RAY DIFFRACTIONf_chiral_restr0.0597890
X-RAY DIFFRACTIONf_plane_restr0.0081072
X-RAY DIFFRACTIONf_dihedral_angle_d7.1832786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.240.47591440.50665237X-RAY DIFFRACTION95.88
2.24-2.270.40131380.48395285X-RAY DIFFRACTION98.07
2.27-2.30.50371360.45465389X-RAY DIFFRACTION98.91
2.3-2.330.45071400.42815385X-RAY DIFFRACTION99.25
2.33-2.370.46871420.41025361X-RAY DIFFRACTION99.21
2.37-2.40.44741460.39015367X-RAY DIFFRACTION99.28
2.4-2.440.4471380.37355474X-RAY DIFFRACTION99.49
2.44-2.480.33271480.35275388X-RAY DIFFRACTION99.62
2.48-2.530.37581420.3395325X-RAY DIFFRACTION99.54
2.53-2.580.32621420.3425416X-RAY DIFFRACTION99.46
2.58-2.630.31031400.32525485X-RAY DIFFRACTION99.38
2.63-2.690.32051440.30185364X-RAY DIFFRACTION99.21
2.69-2.750.31851350.30095401X-RAY DIFFRACTION99.26
2.75-2.820.34831340.30945415X-RAY DIFFRACTION99.71
2.82-2.90.37661420.35393X-RAY DIFFRACTION99.77
2.9-2.980.29071300.27855441X-RAY DIFFRACTION99.48
2.98-3.080.30181420.27515405X-RAY DIFFRACTION99.68
3.08-3.190.25541380.24725406X-RAY DIFFRACTION99.68
3.19-3.310.28941360.24265371X-RAY DIFFRACTION99.87
3.32-3.470.29471440.24325488X-RAY DIFFRACTION99.88
3.47-3.650.26061330.21935392X-RAY DIFFRACTION99.87
3.65-3.880.20771520.19135439X-RAY DIFFRACTION99.93
3.88-4.180.22111380.16475423X-RAY DIFFRACTION100
4.18-4.60.1761400.15915404X-RAY DIFFRACTION100
4.6-5.260.15651360.15475447X-RAY DIFFRACTION99.96
5.26-6.620.19431390.18435439X-RAY DIFFRACTION100
6.63-48.80.18121440.16915421X-RAY DIFFRACTION99.64
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)
11.226545342480.2730751474330.2786031922652.226236011710.5714721065323.06759417642-0.181406074523-0.02264404896080.261146941010.0531208999318-0.0280970170629-0.0345266578133-0.7944510442320.416995980003-2.88184829516E-100.715233396867-0.266687523137-0.1300833077190.583052060844-0.01747256107920.57276481478133.1941287332-26.3024614335-21.0356320347
21.71632609020.24599716652-0.02756439485421.679687469740.264652182583.1858392994-0.06341613399370.132942311803-0.175167918909-0.0015035516724-0.1329203171580.3130156426650.631745669992-0.4398516854723.36045888681E-100.792851550155-0.1408405742580.0219103438390.366933794263-0.1093711466040.62431731999532.4771894537-16.092659589621.3853747922
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 38 - 403 / Label seq-ID: 1 - 366

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain A and resseq 38:403)AA
22(chain B and resseq 38:403)BB

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