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- PDB-7vt6: Crystal structure of CBM deleted MtGlu5 in complex with BGC. -

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Basic information

Entry
Database: PDB / ID: 7vt6
TitleCrystal structure of CBM deleted MtGlu5 in complex with BGC.
ComponentsEndoglucanase H
KeywordsHYDROLASE / cellulase / GH5 / Meiothermus taiwanensis WR-220 / endo-beta-1 / 4-glucanase
Function / homology
Function and homology information


glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / TRYPTOPHAN / Endoglucanase H
Similarity search - Component
Biological speciesMeiothermus taiwanensis WR-220 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsYe, T.J. / Ko, P.T. / Huang, K.F. / Wu, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Synergic action of an inserted carbohydrate-binding module in a glycoside hydrolase family 5 endoglucanase.
Authors: Ye, T.J. / Huang, K.F. / Ko, T.P. / Wu, S.H.
History
DepositionOct 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7375
Polymers39,1691
Non-polymers5694
Water9,710539
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-2 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.683, 75.235, 83.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Endoglucanase H


Mass: 39168.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CBM deleted MtGlu5
Source: (gene. exp.) Meiothermus taiwanensis WR-220 (bacteria)
Production host: Escherichia coli B (bacteria) / References: UniProt: A0A399DY85, cellulase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 38.23 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 20 mM Tris, 100 mM NaCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 45521 / % possible obs: 94.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 13.65 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.031 / Rrim(I) all: 0.062 / Χ2: 1.369 / Net I/σ(I): 33.82
Reflection shellResolution: 1.53→1.58 Å / Rmerge(I) obs: 0.186 / Num. unique obs: 4725 / CC1/2: 0.975 / Rpim(I) all: 0.097 / Rrim(I) all: 0.21 / Χ2: 0.684

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mmu

3mmu


Resolution: 1.53→24.28 Å / SU ML: 0.1199 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.9853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1751 2227 4.9 %
Rwork0.1485 43223 -
obs0.1498 45450 94.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.43 Å2
Refinement stepCycle: LAST / Resolution: 1.53→24.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2584 0 15 539 3138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852695
X-RAY DIFFRACTIONf_angle_d1.1073674
X-RAY DIFFRACTIONf_chiral_restr0.0639372
X-RAY DIFFRACTIONf_plane_restr0.0078482
X-RAY DIFFRACTIONf_dihedral_angle_d23.1054972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.560.1921540.14952769X-RAY DIFFRACTION98.58
1.56-1.60.16481290.13822833X-RAY DIFFRACTION99.93
1.6-1.640.15551590.13632794X-RAY DIFFRACTION100
1.64-1.680.16961420.13742801X-RAY DIFFRACTION100
1.68-1.730.18661310.13482823X-RAY DIFFRACTION99.93
1.73-1.790.14551560.14242803X-RAY DIFFRACTION99.93
1.79-1.850.17581490.13892834X-RAY DIFFRACTION99.77
1.85-1.930.19651410.13882821X-RAY DIFFRACTION99.6
1.93-2.010.18521400.14122821X-RAY DIFFRACTION99.36
2.01-2.120.18581490.14792741X-RAY DIFFRACTION97.34
2.12-2.250.16911240.14622808X-RAY DIFFRACTION97.38
2.25-2.430.18771210.152741X-RAY DIFFRACTION95.5
2.43-2.670.19991410.15742657X-RAY DIFFRACTION92.53
2.67-3.060.1881450.15782492X-RAY DIFFRACTION87
3.06-3.850.16861130.15262220X-RAY DIFFRACTION75.92
3.85-24.280.15461330.15472265X-RAY DIFFRACTION74.77

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