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- PDB-7r2c: Crystal structure of TaCel5A Y200F variant in complex with 2-chlo... -

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Basic information

Entry
Database: PDB / ID: 7r2c
TitleCrystal structure of TaCel5A Y200F variant in complex with 2-chloro-4-nitrophenyl-glucose
ComponentsEGI
KeywordsHYDROLASE / glycoside hydrolase / cellulase / GH5_5 family / GH-A clan / (a/b)8 barrel / Thermoascus aurantiacus
Function / homologyglucan catabolic process / cellulase / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase activity / Glycoside hydrolase superfamily / beta-D-glucopyranose / 2-chloranyl-4-nitro-phenol / cellulase
Function and homology information
Biological speciesThermoascus aurantiacus ATCC 26904 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
AuthorsDutoit, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Other governmentBAG 20191372 Belgium
CitationJournal: To Be Published
Title: Crystal structure of TaCel5A Y200F variant in complex with 2-chloro-4-nitrophenyl-glucose
Authors: Dutoit, R.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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: EGI
B: EGI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,80713
Polymers67,4272
Non-polymers1,38011
Water15,457858
1
A: EGI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5478
Polymers33,7131
Non-polymers8347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EGI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2595
Polymers33,7131
Non-polymers5464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.000, 84.020, 88.930
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 EGI / Endoglucanase


Mass: 33713.328 Da / Num. of mol.: 2 / Mutation: Y200F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus ATCC 26904 (fungus)
Gene: eg1 / Plasmid: pET30b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TG26, cellulase
#2: Chemical ChemComp-P9P / 2-chloranyl-4-nitro-phenol


Mass: 173.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4ClNO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Reservoir solution: 0.1M Tris pH6.5, 1.6M ammonium sulfate Drop: 2 ul of protein solution, 2 ul of reservoir solution, 0.2 ul of microseeds Protein solution: 465 uM enzyme, 5 mM 2-chloro-4- ...Details: Reservoir solution: 0.1M Tris pH6.5, 1.6M ammonium sulfate Drop: 2 ul of protein solution, 2 ul of reservoir solution, 0.2 ul of microseeds Protein solution: 465 uM enzyme, 5 mM 2-chloro-4-nitrophenyl-cellotriose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 8, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.48→44.46 Å / Num. obs: 94541 / % possible obs: 99.7 % / Redundancy: 13.363 % / Biso Wilson estimate: 17.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.108 / Χ2: 0.891 / Net I/σ(I): 14.93 / Num. measured all: 1263352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.48-1.5211.5391.2571.6877057692666780.771.31596.4
1.52-1.5613.3250.9942.4590289677667760.8931.034100
1.56-1.6113.1480.7753.1386333656765660.930.807100
1.61-1.6613.9460.6144.1688964637963790.950.638100
1.66-1.7113.920.5115.0586694622962280.9660.531100
1.71-1.7713.8250.396.583077601060090.9780.405100
1.77-1.8413.7170.3178.1479191577357730.9830.33100
1.84-1.9113.5260.25410.0875896561156110.9880.264100
1.91-213.110.1921370284536153610.9920.2100
2-2.112.8740.15515.9466017512851280.9940.161100
2.1-2.2113.0890.1319.1564162490249020.9960.135100
2.21-2.3413.8410.11621.9263944462046200.9960.121100
2.34-2.5114.2660.09925.2862255436443640.9970.103100
2.51-2.7114.0740.08828.0957704410041000.9970.092100
2.71-2.9713.8070.07831.4251874375737570.9980.081100
2.97-3.3213.3610.06534.8545736342334230.9980.068100
3.32-3.8312.3770.05837.4337639304130410.9980.06100
3.83-4.6912.7630.05141.133146259725970.9990.053100
4.69-6.6313.880.05141.4928219203320330.9990.053100
6.63-44.4612.4440.04740.1514871120011950.9980.04999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.58 Å47.61 Å
Translation3.58 Å47.61 Å

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Processing

Software
NameVersionClassification
XDS20210323data reduction
XSCALE20210323data scaling
PHASER2.8.3phasing
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GZJ

1gzj


Resolution: 1.48→44.46 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1871 4722 5 %
Rwork0.1652 89774 -
obs0.1663 94496 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.27 Å2 / Biso mean: 20.8616 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 1.48→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4754 0 79 858 5691
Biso mean--28.45 31.85 -
Num. residues----610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.50.37291420.39552736287892
1.5-1.520.32031550.314329443099100
1.52-1.540.32021560.2829703126100
1.54-1.560.30751550.266629393094100
1.56-1.580.29861570.236729733130100
1.58-1.60.27621570.22229793136100
1.6-1.620.23791560.200829693125100
1.62-1.640.24721560.194529693125100
1.64-1.670.221560.187629733129100
1.67-1.70.23551560.187829713127100
1.7-1.730.21741580.189929853143100
1.73-1.760.23451560.194429743130100
1.76-1.790.23681550.197229653120100
1.79-1.830.25141590.198630153174100
1.83-1.870.17961550.177229543109100
1.87-1.910.22231580.171929983156100
1.91-1.960.1891560.171929643120100
1.96-2.010.21411570.160929843141100
2.01-2.070.1791580.157930073165100
2.07-2.140.19061570.157229873144100
2.14-2.220.19291590.159130113170100
2.22-2.30.17411570.158329893146100
2.3-2.410.17761600.155330353195100
2.41-2.540.17511580.161630133171100
2.54-2.690.17221590.159230083167100
2.69-2.90.18771590.161130253184100
2.9-3.190.17451600.159230443204100
3.19-3.660.1551620.146730803242100
3.66-4.610.13921620.126130763238100
4.61-44.460.15531710.150932373408100

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