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- PDB-5xd0: Apo Structure of Beta-1,3-1,4-glucanase from Paenibacillus sp.X4 -

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Basic information

Entry
Database: PDB / ID: 5xd0
TitleApo Structure of Beta-1,3-1,4-glucanase from Paenibacillus sp.X4
ComponentsGlucanase
KeywordsHYDROLASE / Beta-1 / 3-1 / 4-glucanase / Glucan Beta-1 / 3 linkage Beta-glucosyl hydrolase
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glucanase
Similarity search - Component
Biological speciesPaenibacillus sp. X4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBaek, S.C. / Ho, T.-H. / Kang, L.-W. / Kim, H.
CitationJournal: Appl. Microbiol. Biotechnol. / Year: 2017
Title: Improvement of enzyme activity of beta-1,3-1,4-glucanase from Paenibacillus sp. X4 by error-prone PCR and structural insights of mutated residues.
Authors: Baek, S.C. / Ho, T.H. / Lee, H.W. / Jung, W.K. / Gang, H.S. / Kang, L.W. / Kim, H.
History
DepositionMar 24, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 19, 2017ID: 5X3A
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucanase
B: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2144
Polymers89,9582
Non-polymers2562
Water5,152286
1
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1292
Polymers44,9791
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0852
Polymers44,9791
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.721, 64.161, 70.502
Angle α, β, γ (deg.)71.04, 77.07, 75.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glucanase / beta-1 / 3-1 / 4-glucanase


Mass: 44978.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. X4 (bacteria) / Strain: X4 / Gene: lic8H / Production host: Escherichia coli (E. coli) / References: UniProt: A0A088BCU2, licheninase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.3 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M amino acids, 12.5%(v/v) MPD, 12.5%(w/v) PEG 1000, 12.5%(w/v) PEG 3350, 0.1 M Tris(base)/Bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2015
RadiationMonochromator: DCM Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.79→65.86 Å / Num. obs: 66856 / % possible obs: 97.5 % / Redundancy: 3.6 % / Net I/σ(I): 25
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3269 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V5C

1v5c


Resolution: 1.79→65.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.156 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18761 3379 5.1 %RANDOM
Rwork0.15098 ---
obs0.15283 63477 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.798 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.79→65.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5860 0 17 286 6163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.026029
X-RAY DIFFRACTIONr_bond_other_d0.0020.025326
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.9158190
X-RAY DIFFRACTIONr_angle_other_deg1.156312268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25425.217276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7315928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.231512
X-RAY DIFFRACTIONr_chiral_restr0.150.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027034
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021474
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.321.3433022
X-RAY DIFFRACTIONr_mcbond_other1.3181.3433021
X-RAY DIFFRACTIONr_mcangle_it1.9172.0083774
X-RAY DIFFRACTIONr_mcangle_other1.9172.0083775
X-RAY DIFFRACTIONr_scbond_it2.1021.5293007
X-RAY DIFFRACTIONr_scbond_other2.0981.5293007
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1592.2024417
X-RAY DIFFRACTIONr_long_range_B_refined3.89911.4417522
X-RAY DIFFRACTIONr_long_range_B_other3.86611.3927489
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.794→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 213 -
Rwork0.188 3971 -
obs--82.18 %

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