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- PDB-3h0o: The importance of CH-Pi stacking interactions between carbohydrat... -

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Basic information

Entry
Database: PDB / ID: 3h0o
TitleThe importance of CH-Pi stacking interactions between carbohydrate and aromatic residues in truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase
ComponentsBeta-glucanase
KeywordsHYDROLASE / 1 / 3-1 / 4-beta-D-Glucanase / CH-Pi stacking interactions / Tris inhibition / Glycosidase
Function / homology
Function and homology information


licheninase activity / licheninase / carbohydrate metabolic process
Similarity search - Function
Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Beta-glucanase
Similarity search - Component
Biological speciesFibrobacter succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTsai, L.C. / Hsiao, C.H.
Citation
Journal: To be Published
Title: The importance of CH-Pi stacking interactions between carbohydrate and aromatic residues in truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase
Authors: Tsai, L.C. / Hsiao, C.H. / Huang, H.C.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase in complex with beta-1,3-1,4-cellotriose
Authors: Tsai, L.C. / Shyur, L.F. / Cheng, Y.S. / Lee, S.H.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a natural circularly permuted jellyroll protein: 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes
Authors: Tsai, L.C. / Shyur, L.F. / Lee, S.H. / Lin, S.S. / Yuan, H.S.
History
DepositionApr 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: 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-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1948
Polymers26,7741
Non-polymers4207
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.4, 68.6, 70.7
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-glucanase / Endo-beta-1 / 3-1 / 4 glucanase / 1 / 3-1 / 4-beta-D-glucan 4-glucanohydrolase / Mixed linkage beta- ...Endo-beta-1 / 3-1 / 4 glucanase / 1 / 3-1 / 4-beta-D-glucan 4-glucanohydrolase / Mixed linkage beta-glucanase / Lichenase


Mass: 26774.445 Da / Num. of mol.: 1 / Mutation: W203F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fibrobacter succinogenes (bacteria) / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17989, licheninase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 295 K / Method: liquid diffusion / pH: 8.5
Details: 24% PEG 5000 MME, 0.5M calcium acetate, 0.35M Tris-HCl, pH8.5, LIQUID DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.65 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2009
RadiationMonochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 1.4→27.87 Å / Num. all: 58660 / Num. obs: 55766 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.047 / Net I/σ(I): 30.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 5718 / Rsym value: 0.455 / % possible all: 98.4

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZM1

1zm1


Resolution: 1.4→27.87 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 277042.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.199 5664 10.2 %RANDOM
Rwork0.179 ---
obs0.179 55766 95.4 %-
all-58660 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.0364 Å2 / ksol: 0.372908 e/Å3
Displacement parametersBiso mean: 15.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2--5.54 Å20 Å2
3----3.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→27.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 23 282 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.482
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.482.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 843 10.1 %
Rwork0.229 7526 -
obs-7526 87.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2act.paramact.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5trs.paramtrs.top

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