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- PDB-7eo3: X-ray structure analysis of beita-1,3-glucanase -

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Basic information

Entry
Database: PDB / ID: 7eo3
TitleX-ray structure analysis of beita-1,3-glucanase
Components1,3-beta-glucanase
KeywordsHYDROLASE / Beita-1 / 3-glucanase / Glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Cellulose binding, type IV / Cellulose Binding Domain Type IV / Glycosyl hydrolases family 16 / Carbohydrate binding module (family 6) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...Cellulose binding, type IV / Cellulose Binding Domain Type IV / Glycosyl hydrolases family 16 / Carbohydrate binding module (family 6) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesActinobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.141 Å
AuthorsWan, Q. / Feng, J. / Xu, S.
CitationJournal: Bioresour Bioprocess / Year: 2021
Title: Identification and structural analysis of a thermophilic beta-1,3-glucanase from compost
Authors: Feng, J. / Xu, S. / Feng, R. / Kovalevsky, A. / Zhang, X. / Liu, D. / Wan, Q.
History
DepositionApr 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,3-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0083
Polymers30,8621
Non-polymers1462
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.397, 61.010, 70.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 1,3-beta-glucanase


Mass: 30861.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacteria bacterium (bacteria) / Gene: DIU60_04100
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2W4NIL6
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Magnesium chloride, Bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→50 Å / Num. obs: 95197 / % possible obs: 100 % / Redundancy: 11.5 % / Biso Wilson estimate: 13.64 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.042 / Rrim(I) all: 0.15 / Χ2: 1.034 / Net I/σ(I): 4.6 / Num. measured all: 1099159
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.14-1.168.30.86547030.7560.320.9241.069100
1.16-1.1890.81947100.8060.2890.871.065100
1.18-1.210.10.81646940.8280.2660.8591.045100
1.2-1.2310.60.80447120.8830.2540.8441.056100
1.23-1.2510.90.7947020.8830.2460.8281.063100
1.25-1.28110.74647110.8990.230.7821.061100
1.28-1.3210.70.67747210.9150.2130.711.04100
1.32-1.3511.10.64247340.9180.1980.6721.045100
1.35-1.3912.20.58647030.9470.170.611.025100
1.39-1.4412.20.50747490.9570.1460.5281.051100
1.44-1.4912.40.44347070.9650.1280.4611.046100
1.49-1.5512.20.36347480.9730.1060.3781.032100
1.55-1.6211.60.29147490.9770.0880.3051.024100
1.62-1.712.50.25547560.9850.0740.2661.029100
1.7-1.8113.20.21547710.9860.0610.2241.017100
1.81-1.95130.17847880.9890.050.1851.005100
1.95-2.1512.40.1548040.9910.0440.1571.043100
2.15-2.4612.20.13348200.9880.040.1381.028100
2.46-3.0913.30.11548730.9940.0330.1190.98100
3.09-5011.90.10650420.9910.0320.1111.0199.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DGT

3dgt


Resolution: 1.141→16.92 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1618 4741 5 %RANDOM
Rwork0.1434 90117 --
obs0.1443 94858 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.06 Å2 / Biso mean: 16.5594 Å2 / Biso min: 10.18 Å2
Refinement stepCycle: final / Resolution: 1.141→16.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 9 297 2478
Biso mean--19.87 28.73 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052314
X-RAY DIFFRACTIONf_angle_d0.9423183
X-RAY DIFFRACTIONf_chiral_restr0.089318
X-RAY DIFFRACTIONf_plane_restr0.006423
X-RAY DIFFRACTIONf_dihedral_angle_d5.3161706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.141-1.15380.27181490.2254260488
1.1538-1.16740.22241550.2085291598
1.1674-1.18160.21561740.1934295599
1.1816-1.19660.21711610.1842295299
1.1966-1.21230.17931700.1793293599
1.2123-1.22890.23281460.17733003100
1.2289-1.24650.22551280.17553000100
1.2465-1.26510.19031450.1693000100
1.2651-1.28480.19121620.15672998100
1.2848-1.30590.20621390.15382998100
1.3059-1.32840.15981440.14733021100
1.3284-1.35250.17121740.14472962100
1.3525-1.37850.17551700.14122987100
1.3785-1.40670.16661570.13643027100
1.4067-1.43720.14591420.12463008100
1.4372-1.47070.14891650.11782983100
1.4707-1.50740.13271720.1193023100
1.5074-1.54810.13981410.12083005100
1.5481-1.59370.15891510.12023015100
1.5937-1.64510.1511590.12333028100
1.6451-1.70380.15321750.11942992100
1.7038-1.7720.15141480.12763046100
1.772-1.85250.18821400.13013058100
1.8525-1.950.14161670.13793039100
1.95-2.0720.15121640.1343018100
2.072-2.23170.15031530.13883069100
2.2317-2.45560.1641480.14893077100
2.4556-2.80960.17031620.15283075100
2.8096-3.53450.17261970.15513088100
3.5345-16.920.14591830.14283236100

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