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- PDB-7vt8: Crystal structure of MtGlu5 from Meiothermus taiwanensis WR-220 -

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Basic information

Entry
Database: PDB / ID: 7vt8
TitleCrystal structure of MtGlu5 from Meiothermus taiwanensis WR-220
ComponentsEndoglucanase H
KeywordsHYDROLASE / cellulase / GH5 / Meiothermus taiwanensis WR-220 / endo-beta-1 / 4-glucanase
Function / homology
Function and homology information


cellulase / cellulase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / Endoglucanase H
Similarity search - Component
Biological speciesMeiothermus taiwanensis WR-220 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,92610
Polymers52,9771
Non-polymers9499
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.929, 144.929, 197.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Endoglucanase H


Mass: 52977.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 4.9 Å3/Da / Density % sol: 74.88 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 0.16M citric acid, 1.1M ammonium sulfate, 10% PEG-400, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 21603 / % possible obs: 99.8 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.027 / Rrim(I) all: 0.076 / Χ2: 0.781 / Net I/σ(I): 26.55
Reflection shellResolution: 2.99→3.04 Å / Num. unique obs: 1055 / CC1/2: 0.866 / Rpim(I) all: 0.439 / Χ2: 0.657

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mmu

3mmu


Resolution: 2.99→29.21 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1074 4.99 %
Rwork0.2055 20441 -
obs0.2077 21515 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 259.62 Å2 / Biso mean: 118.445 Å2 / Biso min: 47.66 Å2
Refinement stepCycle: final / Resolution: 2.99→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 52 36 3606
Biso mean--164.37 90.12 -
Num. residues----437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.99-3.120.37431310.38052427255896
3.12-3.290.34851320.30582530266299
3.29-3.490.30781320.25722495262799
3.49-3.760.26211340.23725542688100
3.76-4.140.21391370.187625472684100
4.14-4.740.22831290.174525742703100
4.74-5.960.22381360.193725892725100
5.96-29.210.24281430.183427252868100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4157-0.0242-0.96261.50970.45372.0024-0.0931-0.09930.1713-0.05970.02910.0860.052-0.2043-0.00010.4703-0.08610.06660.7426-0.00090.518646.466165.033917.4011
20.12660.4687-0.1749-0.1282-0.68720.086-0.06110.32360.016-0.6449-0.012-0.0370.184-0.0251-01.1477-0.17090.22571.0350.18931.12252.010334.118526.7987
30.09460.825-0.20241.1247-1.07780.9624-0.3309-0.3534-0.0683-0.26610.2824-0.0334-0.2819-0.6704-0.06450.7232-0.31120.23970.98580.11230.96747.452537.582535.2936
40.2009-0.07120.09040.0933-0.16770.07670.34020.0532-0.1863-0.51870.18190.2202-1.08370.42860.00020.8578-0.14960.08690.934-0.00270.987133.509450.66911.6153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 218 )A17 - 218
2X-RAY DIFFRACTION2chain 'A' and (resid 219 through 285 )A219 - 285
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 418 )A286 - 418
4X-RAY DIFFRACTION4chain 'A' and (resid 419 through 453 )A419 - 453

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