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- PDB-3hr9: The truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase F... -

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Basic information

Entry
Database: PDB / ID: 3hr9
TitleThe truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase F40I mutant
ComponentsBeta-glucanase
KeywordsHYDROLASE / 1 / 3-1 / 4-beta-D-Glucanase / carbohydrate 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTsai, L.C. / Huang, H.C. / Hsiao, C.H.
Citation
Journal: To be Published
Title: The truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase mutant F40I
Authors: Tsai, L.C. / Huang, H.C. / Je-Hsin, C. / Lie-Fen, S.
#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
DepositionJun 9, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionJul 7, 2009ID: 2R4A
Revision 1.0Jul 7, 2009Provider: 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.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _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)27,2868
Polymers26,8671
Non-polymers4207
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.300, 68.030, 70.460
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: 26866.543 Da / Num. of mol.: 1 / Fragment: UNP residues 26-266 / Mutation: F40I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fibrobacter succinogenes (bacteria) / Gene: succinogenes / 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.: 242 / 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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 295 K / Method: liquid diffusion / pH: 8.5
Details: 24% PEG5KMME, 0.5M calcium acetate, 0.35M Tris-HCl, pH8.5, LIQUID DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 17, 2006
RadiationMonochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→27.77 Å / Num. all: 32440 / Num. obs: 31160 / % possible obs: 95.7 % / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 62.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 10 % / Mean I/σ(I) obs: 9.6 / Num. unique all: 3203 / Rsym value: 0.347 / % possible all: 100

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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: 1.7→27.77 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 224067.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3102 10 %RANDOM
Rwork0.193 ---
obs0.193 31160 95.6 %-
all-32440 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.5513 Å2 / ksol: 0.453006 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2--5.64 Å20 Å2
3----3.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 23 242 2163
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.452 456 9.5 %
Rwork0.41 4369 -
obs--90.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate-link.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5trs-act.paramtrs-act.top

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