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- PDB-7quz: Crystal structure of the SeMet octameric C-terminal Big_2-CBM56 d... -

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Basic information

Entry
Database: PDB / ID: 7quz
TitleCrystal structure of the SeMet octameric 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
Biological speciesPaenibacillus illinoisensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.156 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 Bacillus circulans 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
DepositionJan 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Author supporting evidence / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_audit_support
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_audit_support.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-1,3-glucanase bglH
BBB: Beta-1,3-glucanase bglH
CCC: Beta-1,3-glucanase bglH
DDD: Beta-1,3-glucanase bglH
EEE: Beta-1,3-glucanase bglH
FFF: Beta-1,3-glucanase bglH
GGG: Beta-1,3-glucanase bglH
HHH: Beta-1,3-glucanase bglH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,54828
Polymers172,3868
Non-polymers1,16220
Water14,340796
1
AAA: Beta-1,3-glucanase bglH
BBB: Beta-1,3-glucanase bglH
hetero molecules

AAA: Beta-1,3-glucanase bglH
BBB: Beta-1,3-glucanase bglH
hetero molecules


  • defined by author
  • Evidence: homology, There are two other crystals forms which also display the tetrameric form.
  • 87.1 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)87,14218
Polymers86,1934
Non-polymers94914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11300 Å2
ΔGint-116 kcal/mol
Surface area31040 Å2
2
CCC: Beta-1,3-glucanase bglH
DDD: Beta-1,3-glucanase bglH
hetero molecules

CCC: Beta-1,3-glucanase bglH
DDD: Beta-1,3-glucanase bglH
hetero molecules


  • defined by author
  • 86.8 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)86,77414
Polymers86,1934
Non-polymers58110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10200 Å2
ΔGint-108 kcal/mol
Surface area31200 Å2
3
EEE: Beta-1,3-glucanase bglH
FFF: Beta-1,3-glucanase bglH
GGG: Beta-1,3-glucanase bglH
HHH: Beta-1,3-glucanase bglH
hetero molecules


  • defined by author
  • 86.6 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)86,59012
Polymers86,1934
Non-polymers3978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-112 kcal/mol
Surface area31350 Å2
Unit cell
Length a, b, c (Å)201.125, 51.716, 168.659
Angle α, β, γ (deg.)90.000, 92.494, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-413-

HOH

21CCC-426-

HOH

31CCC-507-

HOH

41DDD-505-

HOH

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Components

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


Mass: 21548.229 Da / Num. of mol.: 8
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: PET-28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: Q45095
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein concentration 30.0 mg/ml, 0.1 M Magnesium Chloride hexahydrate, 0.1 M HEPES pH 7.5, PEG 400 with 30% glycerol added to crystallisation buffer for cryocooling.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→48.772 Å / Num. obs: 94220 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.982 / Rmerge(I) obs: 0.336 / Rpim(I) all: 0.265 / Rrim(I) all: 0.429 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
11.8-48.7240.0576490.9980.0460.074
2.15-2.193.63.80241440.1633.1614.967

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
CRANK22.0.25phasing
MOLREP2.0.25phasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.156→48.771 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 19.895 / SU ML: 0.245 / Cross valid method: FREE R-VALUE / ESU R: 0.274 / ESU R Free: 0.232
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2924 4797 5.093 %
Rwork0.2397 89388 -
all0.242 --
obs-94185 99.747 %
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: 26.918 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å2-0.732 Å2
2---0.491 Å2-0 Å2
3----0.433 Å2
Refinement stepCycle: LAST / Resolution: 2.156→48.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10726 0 60 796 11582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01311058
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710146
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.64815223
X-RAY DIFFRACTIONr_angle_other_deg1.271.57123356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6651479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.03426.667420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.483151471
X-RAY DIFFRACTIONr_chiral_restr0.0690.21562
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022338
X-RAY DIFFRACTIONr_nbd_refined0.1890.21708
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.28840
X-RAY DIFFRACTIONr_nbtor_refined0.1620.25119
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.25438
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2612
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.299
X-RAY DIFFRACTIONr_nbd_other0.2530.2245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.257
X-RAY DIFFRACTIONr_mcbond_it0.8141.4545910
X-RAY DIFFRACTIONr_mcbond_other0.8141.4535909
X-RAY DIFFRACTIONr_mcangle_it1.4652.1737376
X-RAY DIFFRACTIONr_mcangle_other1.4652.1737377
X-RAY DIFFRACTIONr_scbond_it0.8741.5365145
X-RAY DIFFRACTIONr_scbond_other0.8741.5375146
X-RAY DIFFRACTIONr_scangle_it1.4512.2737842
X-RAY DIFFRACTIONr_scangle_other1.4512.2737843
X-RAY DIFFRACTIONr_lrange_it4.04217.64111201
X-RAY DIFFRACTIONr_lrange_other3.97417.4611068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.156-2.2120.4443470.4446322X-RAY DIFFRACTION97.2016
2.212-2.2720.4063610.3936387X-RAY DIFFRACTION99.9408
2.272-2.3380.3883240.366264X-RAY DIFFRACTION100
2.338-2.410.3743060.3486057X-RAY DIFFRACTION99.9372
2.41-2.4890.3913390.3365859X-RAY DIFFRACTION100
2.489-2.5770.3962870.3085689X-RAY DIFFRACTION99.9833
2.577-2.6740.352810.2855504X-RAY DIFFRACTION100
2.674-2.7830.312870.2465269X-RAY DIFFRACTION99.964
2.783-2.9070.3032670.2315113X-RAY DIFFRACTION100
2.907-3.0490.2552540.2124895X-RAY DIFFRACTION99.9806
3.049-3.2140.2832350.1964611X-RAY DIFFRACTION100
3.214-3.4080.2632420.1944379X-RAY DIFFRACTION100
3.408-3.6440.2632020.1964140X-RAY DIFFRACTION100
3.644-3.9350.2592180.1933823X-RAY DIFFRACTION100
3.935-4.3110.2312270.1613565X-RAY DIFFRACTION100
4.311-4.8190.1611800.1293176X-RAY DIFFRACTION100
4.819-5.5640.1881490.1572865X-RAY DIFFRACTION99.9337
5.564-6.8130.2681270.1682445X-RAY DIFFRACTION100
6.813-9.6270.2261150.1511902X-RAY DIFFRACTION99.9504
9.627-48.7710.249490.2051117X-RAY DIFFRACTION98.9813
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)
11.2953-0.5433-1.86310.56270.78443.27740.0063-0.14030.08680.05950.0857-0.1199-0.00080.2308-0.0920.1585-0.00130.07830.0189-0.01820.08739.5447-25.35831.1741
20.6711-0.3102-1.18160.59030.7323.5814-0.0528-0.09960.01090.07170.1108-0.13330.23980.2596-0.0580.1760.0250.06470.0266-0.0170.07617.4584-46.95186.21
31.16090.4334-1.77890.573-0.76213.362-0.00330.11190.0626-0.07530.07240.11290.0309-0.226-0.06920.151-0.00180.06170.01940.01180.0702-13.1778-51.375182.6879
40.80180.287-1.27610.7976-0.74153.4509-0.04750.1353-0.021-0.07560.08390.17150.2514-0.2649-0.03650.2042-0.0260.07660.0262-00.092-10.8632-72.90177.4537
50.6696-0.3608-0.82670.82941.11523.6385-0.017-0.07080.09290.01910.0999-0.1138-0.15920.281-0.0830.1333-0.03720.09280.0644-0.00830.1428-42.0364-83.53841.9557
60.67310.1091-0.52940.7258-0.7993.87640.03440.1033-0.0324-0.06530.13940.16840.2463-0.2742-0.17380.144-0.02580.08060.0717-0.0170.1608-60.4408-105.081239.4412
70.87340.2378-1.02820.8145-0.77833.683-0.00610.04870.0717-0.00720.09220.1272-0.0995-0.2508-0.08620.10580.0270.08540.03840.00980.1629-61.1436-83.531444.3837
80.62140.0094-0.50750.78530.95524.6732-0.0184-0.07120.02880.1110.1012-0.18620.24730.2459-0.08280.14230.04720.07220.04160.00740.1664-42.7708-104.992747.0346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA24 - 207
2X-RAY DIFFRACTION2ALLBBB22 - 207
3X-RAY DIFFRACTION3ALLCCC24 - 207
4X-RAY DIFFRACTION4ALLDDD21 - 207
5X-RAY DIFFRACTION5ALLEEE24 - 207
6X-RAY DIFFRACTION6ALLFFF24 - 207
7X-RAY DIFFRACTION7ALLGGG24 - 207
8X-RAY DIFFRACTION8ALLHHH24 - 207

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