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- PDB-3axd: The truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase V... -

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Basic information

Entry
Database: PDB / ID: 3axd
TitleThe truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase V18Y/W203Y in apo-form
ComponentsBeta-glucanase
KeywordsHYDROLASE / glucanase / cellobiose/cellotetraose
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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesFibrobacter succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsHuang, J.W. / Cheng, Y.S. / Ko, T.P. / Lin, C.Y. / Lai, H.L. / Chen, C.C. / Ma, Y. / Huang, C.H. / Zheng, Y. / Liu, J.R. / Guo, R.T.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2012
Title: Rational design to improve thermostability and specific activity of the truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase
Authors: Huang, J.W. / Cheng, Y.S. / Ko, T.P. / Lin, C.Y. / Lai, H.L. / Chen, C.C. / Ma, Y. / Zheng, Y. / Huang, C.H. / Zou, P. / Liu, J.R. / Guo, R.T.
History
DepositionApr 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucanase
B: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,22012
Polymers55,6552
Non-polymers56510
Water12,538696
1
A: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1908
Polymers27,8281
Non-polymers3637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0304
Polymers27,8281
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.391, 69.963, 81.242
Angle α, β, γ (deg.)90.00, 100.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27827.656 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-271 / Mutation: V18Y, W203Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fibrobacter succinogenes (bacteria) / Strain: ATCC 19169, S85 / Gene: Fisuc_2961, FSU_0226 / Plasmid: pET 32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17989, licheninase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris-HCl, pH 7.5, 0.3M Calcium actetate, 29% PEG5KMME, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→25 Å / Num. all: 66972 / Num. obs: 66704 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 33.5
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 7.4 / Num. unique all: 6700 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
XTALVIEWrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZM1

1zm1


Resolution: 1.53→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3351 -RANDOM
Rwork0.173 ---
all-66972 --
obs-66001 98.6 %-
Displacement parametersBiso mean: 14.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati sigma a obs: 0.06 Å
Refinement stepCycle: LAST / Resolution: 1.53→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 24 696 4485
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 1.53→1.58 Å
RfactorNum. reflection% reflection
Rfree0.243 340 -
Rwork0.207 --
obs-6425 96.37 %

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