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- PDB-9bjx: GH5_4 endo-beta(1,3/1,4)-glucanase from Segatella copri -

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Basic information

Entry
Database: PDB / ID: 9bjx
TitleGH5_4 endo-beta(1,3/1,4)-glucanase from Segatella copri
ComponentsCellulase (Glycosyl hydrolase family 5)
KeywordsHYDROLASE / mixed-linkage beta-glucan / MLG / GH5_4
Function / homology: / glucan catabolic process / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / beta-glucosidase activity / Glycoside hydrolase superfamily / cell surface / extracellular region / Cellulase (Glycosyl hydrolase family 5)
Function and homology information
Biological speciesSegatella copri DSM 18205 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionApr 25, 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)
C: Cellulase (Glycosyl hydrolase family 5)
D: Cellulase (Glycosyl hydrolase family 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,3189
Polymers168,0084
Non-polymers3105
Water12,142674
1
A: Cellulase (Glycosyl hydrolase family 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0642
Polymers42,0021
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulase (Glycosyl hydrolase family 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1263
Polymers42,0021
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cellulase (Glycosyl hydrolase family 5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1263
Polymers42,0021
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cellulase (Glycosyl hydrolase family 5)


Theoretical massNumber of molelcules
Total (without water)42,0021
Polymers42,0021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.008, 51.560, 157.057
Angle α, β, γ (deg.)90.000, 101.500, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Cellulase (Glycosyl hydrolase family 5)


Mass: 42001.891 Da / Num. of mol.: 4
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M LiCl, 19% (w/v) Polyethylene glycol 3,350 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→38.95 Å / Num. obs: 197039 / % possible obs: 97.79 % / Redundancy: 2 % / Biso Wilson estimate: 18.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02492 / Net I/σ(I): 14.59
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.3104 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 19223 / CC1/2: 0.826 / % possible all: 96.03

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.95 Å / SU ML: 0.1647 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 10002 5.08 %RANDOM
Rwork0.1769 186943 --
obs0.178 196945 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.65 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11826 0 20 674 12520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006312596
X-RAY DIFFRACTIONf_angle_d0.838417152
X-RAY DIFFRACTIONf_chiral_restr0.05731722
X-RAY DIFFRACTIONf_plane_restr0.00852257
X-RAY DIFFRACTIONf_dihedral_angle_d6.13091676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.29083170.25936046X-RAY DIFFRACTION94.74
1.62-1.640.27633230.23786000X-RAY DIFFRACTION95.98
1.64-1.660.29143040.22956228X-RAY DIFFRACTION97.38
1.66-1.680.25612970.22036170X-RAY DIFFRACTION97.51
1.68-1.70.24123310.21136215X-RAY DIFFRACTION97.89
1.7-1.720.23153600.20146206X-RAY DIFFRACTION97.68
1.72-1.750.22283260.20196118X-RAY DIFFRACTION97.78
1.75-1.770.21593200.19526297X-RAY DIFFRACTION98.02
1.77-1.80.22793310.1896156X-RAY DIFFRACTION97.86
1.8-1.830.20243480.18746207X-RAY DIFFRACTION97.97
1.83-1.860.22523650.1876194X-RAY DIFFRACTION97.98
1.86-1.90.21443400.18126188X-RAY DIFFRACTION97.75
1.9-1.930.20393360.17746106X-RAY DIFFRACTION97.33
1.93-1.970.20653230.17315941X-RAY DIFFRACTION93.45
1.97-2.020.20463230.17116165X-RAY DIFFRACTION97.05
2.02-2.060.20053600.16836262X-RAY DIFFRACTION98.35
2.06-2.110.19823390.176241X-RAY DIFFRACTION98.52
2.11-2.170.213230.16756257X-RAY DIFFRACTION98.74
2.17-2.240.19893200.16736353X-RAY DIFFRACTION98.8
2.24-2.310.19773240.16856260X-RAY DIFFRACTION98.77
2.31-2.390.20323380.16976276X-RAY DIFFRACTION98.72
2.39-2.490.19783670.16566252X-RAY DIFFRACTION98.7
2.49-2.60.19493180.17016316X-RAY DIFFRACTION98.97
2.6-2.740.19983490.1716318X-RAY DIFFRACTION98.54
2.74-2.910.20233140.17636045X-RAY DIFFRACTION94.45
2.91-3.130.19293170.17686411X-RAY DIFFRACTION99.39
3.13-3.450.20213530.17356416X-RAY DIFFRACTION99.6
3.45-3.940.19653410.17246405X-RAY DIFFRACTION99.81
3.94-4.970.17153450.15976414X-RAY DIFFRACTION99.09
4.97-38.950.17883500.18776480X-RAY DIFFRACTION97.06
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)
10.722942161284-0.2136046396790.6488117425820.993246058028-0.2170209269341.940045589-0.005659464095810.01740861233950.02217411056290.0145682284433-0.0204342137658-0.026513103287-0.0324950157885-0.03116481173350.0216366747330.104825933849-0.04726105583190.007347733687270.1522567022650.008356980222280.0957797237621-0.3337106817020.67776811184759.1779652464
20.4307786984070.07038038794260.234114137751.711898073160.1763605704820.6867305002030.00959130928641-0.04372546830390.0120942633614-0.0319560318373-0.04811940402390.0172812656443-0.00529072069952-0.02596729807790.0343745468090.08224361901160.01187441592450.06279835611280.1667251780980.001984201296280.103109919728-17.13788453630.79015244441515.1484151527
31.37481457726-0.06154415576811.453220139681.43349335920.05182978326022.683542881510.04908988382060.104903612755-0.0266115443045-0.07331027717490.0259895354784-0.0447904458690.1135415502510.0815872420307-0.06739360469780.0726205938151-0.006421214045030.009301509145920.1662395421610.01342793559460.121718203508-46.595205089418.182353119461.4150194444
40.881351930914-0.2285087667710.4799296235381.0461436191-0.1597466715711.2661271971-0.0199413469761-0.1168726321060.02559648403160.1232892441890.0573523445414-0.0192665561910.00259357060698-0.036437281788-0.03762608174330.1419482443830.000830344531388-0.01073082008060.159952425454-0.01307129936880.126942395071-66.49733209617.970300302918.8446746683
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 38:405)AA38 - 4051 - 368
22(chain B and resseq 38:405)BB38 - 4051 - 368
33(chain C and resseq 39:404)CC39 - 4041 - 366
44(chain D and resseq 39:404)DD39 - 4041 - 366

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