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- PDB-7r3t: Crystal structure of the Dimeric C-terminal Big_2-CBM56 domains f... -

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Basic information

Entry
Database: PDB / ID: 7r3t
TitleCrystal structure of the Dimeric C-terminal Big_2-CBM56 domains from Paenibacillus illinoisensis (Bacillus circulans IAM1165) beta-1,3-glucanase H
ComponentsBeta-1,3-glucanase bglH
KeywordsHYDROLASE / laminarinase / GH16 sub-family 8 / Big_2 / CBM56
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / CBM56 (carbohydrate binding type-56) domain profile. / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Bacterial Ig-like domain 2 ...: / CBM56 (carbohydrate binding type-56) domain profile. / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-PG6 / Beta-1,3-glucanase
Similarity search - Component
Biological speciesPaenibacillus illinoisensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.109 Å
AuthorsNajmudin, S. / Venditto, I. / Fontes, C.M.G.A. / Bule, P.
Funding support Portugal, European Union, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-PRO/103980/2008 Portugal
European Communitys Seventh Framework Programme263916European Union
CitationJournal: To be published
Title: Structural and biochemical characterization of C-terminal Big_2-CBM56 domains of Paenibacillus illinoisensis IAM1165 beta-1,3-glucanase H and Paenibacillus sp CBM56
Authors: Najmudin, S. / Venditto, I. / Pires, V.R. / Caseiro, C. / Correia, M.A.S. / Romao, M.J. / Carvalho, A.L. / Fontes, C.M.G.A. / Bule, P.
History
DepositionFeb 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-glucanase bglH
B: Beta-1,3-glucanase bglH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5669
Polymers42,8152
Non-polymers7517
Water1,910106
1
A: Beta-1,3-glucanase bglH
B: Beta-1,3-glucanase bglH
hetero molecules

A: Beta-1,3-glucanase bglH
B: Beta-1,3-glucanase bglH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,13218
Polymers85,6304
Non-polymers1,50214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area11630 Å2
ΔGint-96 kcal/mol
Surface area31530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.630, 76.380, 106.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-453-

HOH

31B-443-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-1,3-glucanase bglH


Mass: 21407.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal Big_2-CBM56 domains / Source: (gene. exp.) Paenibacillus illinoisensis (bacteria) / Gene: bglH, beta-1,3-glucanase / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45095

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Non-polymers , 5 types, 113 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20/30/50 mg/ml Protein concentration in 0.2 Magnesium chloride hexahydrate, 0.1 M HEPES sodium salt pH 7.5. 30% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.109→50.63 Å / Num. obs: 22371 / % possible obs: 91.9 % / Redundancy: 3.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.1 / Rrim(I) all: 0.148 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.95-50.633.40.0283630.9990.0240.037
2.11-2.1730.8815660.3650.8061.197

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QUZ

7quz


Resolution: 2.109→45.797 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.886 / SU B: 17.446 / SU ML: 0.217 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.239
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2962 1055 4.719 %
Rwork0.2206 21303 -
all0.224 --
obs-22358 90.934 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.116 Å2
Baniso -1Baniso -2Baniso -3
1-1.529 Å20 Å20 Å2
2---0.605 Å20 Å2
3----0.924 Å2
Refinement stepCycle: LAST / Resolution: 2.109→45.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 46 106 2818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132781
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152582
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.6493818
X-RAY DIFFRACTIONr_angle_other_deg1.3151.575950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8085371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.86626.731104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36815376
X-RAY DIFFRACTIONr_chiral_restr0.0760.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023246
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02578
X-RAY DIFFRACTIONr_nbd_refined0.2050.2510
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.22517
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21307
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1230.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.257
X-RAY DIFFRACTIONr_nbd_other0.2420.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2440.218
X-RAY DIFFRACTIONr_mcbond_it1.282.3651472
X-RAY DIFFRACTIONr_mcbond_other1.2792.3641471
X-RAY DIFFRACTIONr_mcangle_it2.13.5391838
X-RAY DIFFRACTIONr_mcangle_other2.13.5411839
X-RAY DIFFRACTIONr_scbond_it1.3732.5521307
X-RAY DIFFRACTIONr_scbond_other1.3722.5541308
X-RAY DIFFRACTIONr_scangle_it2.2843.7631977
X-RAY DIFFRACTIONr_scangle_other2.2843.7651978
X-RAY DIFFRACTIONr_lrange_it4.27328.9622851
X-RAY DIFFRACTIONr_lrange_other4.24228.8772834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.109-2.1640.332570.3591351X-RAY DIFFRACTION80
2.164-2.2230.339610.321356X-RAY DIFFRACTION80.7407
2.223-2.2870.374770.3011326X-RAY DIFFRACTION83.2641
2.287-2.3580.298680.2761339X-RAY DIFFRACTION85.4281
2.358-2.4350.323690.2671344X-RAY DIFFRACTION87.4381
2.435-2.5210.359590.2761329X-RAY DIFFRACTION89.7801
2.521-2.6160.331860.2681305X-RAY DIFFRACTION92.8571
2.616-2.7220.298580.2431303X-RAY DIFFRACTION94.7112
2.722-2.8430.365670.2291269X-RAY DIFFRACTION96.8116
2.843-2.9820.374630.2261236X-RAY DIFFRACTION96.365
2.982-3.1430.354500.2071167X-RAY DIFFRACTION96.1295
3.143-3.3340.34450.2081117X-RAY DIFFRACTION96.995
3.334-3.5640.193540.2071041X-RAY DIFFRACTION97.1606
3.564-3.8490.266530.191984X-RAY DIFFRACTION96.7351
3.849-4.2160.242560.186890X-RAY DIFFRACTION95.6522
4.216-4.7120.259330.158811X-RAY DIFFRACTION95.0451
4.712-5.4390.242380.174713X-RAY DIFFRACTION93.9925
5.439-6.6580.276310.201605X-RAY DIFFRACTION92.1739
6.658-9.3970.285220.178508X-RAY DIFFRACTION97.2477
9.397-45.7970.54280.233309X-RAY DIFFRACTION94.3452
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)
10.4845-0.45640.96080.8992-1.06845.10120.0460.0148-0.1257-0.06610.0640.10810.5896-0.5316-0.10990.0822-0.08750.00920.1371-0.01680.043-13.8751-9.60511.23
20.87240.10120.79550.8897-0.15775.26650.05370.077-0.1309-0.1783-0.1086-0.0430.63220.56070.05490.10520.08420.01760.07650.00930.02677.2666-8.972-2.9626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA24 - 207
2X-RAY DIFFRACTION1ALLA301
3X-RAY DIFFRACTION2ALLB25 - 207
4X-RAY DIFFRACTION2ALLB303

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