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- PDB-9f0n: Crystal structure of Ta_Cel5A E133A variant, apoform -

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Basic information

Entry
Database: PDB / ID: 9f0n
TitleCrystal structure of Ta_Cel5A E133A variant, apoform
Componentscellulase
KeywordsHYDROLASE / cellulase / TIM barrel
Function / homologyglucan catabolic process / cellulase / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase activity / Glycoside hydrolase superfamily / cellulase
Function and homology information
Biological speciesThermoascus aurantiacus ATCC 26904 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsDutoit, R.
Funding support1items
OrganizationGrant numberCountry
Other governmentBAG 20210875
CitationJournal: To Be Published
Title: Crystal structure of Ta_Cel5A E133A variant, apoform
Authors: Dutoit, R.
History
DepositionApr 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cellulase
B: cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,63013
Polymers67,6052
Non-polymers1,02511
Water13,385743
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Ta_Cel5A eluted as a monomer using a Superdex 75 column (Cytiva) conditioned in 50 mM Tris 150 mM NaCl pH 8.0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-42 kcal/mol
Surface area21690 Å2
Unit cell
Length a, b, c (Å)76.560, 84.920, 89.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cellulase


Mass: 33802.488 Da / Num. of mol.: 2 / Mutation: E133A
Source method: isolated from a genetically manipulated source
Details: Mutation E133A, no tag
Source: (gene. exp.) Thermoascus aurantiacus ATCC 26904 (fungus)
Gene: eg1 / Plasmid: pET30b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8TG26, cellulase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Reservoir solution: 0.1 M Tris pH 6.0, 1.3 M ammonium sulfate. Drop: 2 ul of 430 uM protein, 2 ul of reservoir solution, 0.2 ul of microseeds

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2022
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.18→47.96 Å / Num. obs: 190898 / % possible obs: 99.8 % / Redundancy: 12.2 % / Biso Wilson estimate: 9.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.18 / Rrim(I) all: 0.187 / Net I/σ(I): 15.79
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.18-1.211.814136760.6751.9151
1.21-1.241.693136630.7581.7761
1.24-1.281.573132870.8441.6431
1.28-1.321.421129390.8621.4921
1.32-1.361.296124960.8861.3611
1.36-1.411.133121450.9281.191
1.41-1.461.007117490.9531.0541
1.46-1.520.849112750.9740.8831
1.52-1.590.703108490.9840.7311
1.59-1.670.57103790.9890.5931
1.67-1.760.45398330.9940.4711
1.76-1.860.34293860.9970.3551
1.86-1.990.24587930.9980.2541
1.99-2.150.16682170.9980.1731
2.15-2.360.13575970.9980.1411
2.36-2.640.10368780.9990.1081
2.64-3.040.07861010.9990.0811
3.04-3.730.05252040.9990.0551
3.73-5.270.03940710.9990.0411
5.27-47.960.03723600.9990.0391

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Processing

Software
NameVersionClassification
PHENIX1.21-5207-000refinement
XSCALE20220220data scaling
XDS20220220data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→39.51 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.21
Details: TLS were used in refinement TLS DETAILS. NUMBER OF TLS GROUPS: 14 ORIGIN: CENTER OF MASS TLS GROUP : 1 SELECTION: chain 'A' and (resid 2 through 20 ) ORIGIN FOR THE GROUP (A): -4.2853 16. ...Details: TLS were used in refinement TLS DETAILS. NUMBER OF TLS GROUPS: 14 ORIGIN: CENTER OF MASS TLS GROUP : 1 SELECTION: chain 'A' and (resid 2 through 20 ) ORIGIN FOR THE GROUP (A): -4.2853 16.1391 -9.9754 T TENSOR T11: 0.1188 T22: 0.0976 T33: 0.1119 T12: 0.0019 T13: -0.0172 T23: -0.0058 L TENSOR L11: 0.0482 L22: 0.0724 L33: 0.1579 L12: 0.0530 L13: 0.0365 L23: 0.1188 S TENSOR S11: 0.0107 S12: -0.0623 S13: -0.1541 S21: 0.0032 S22: -0.0374 S23: -0.0269 S31: 0.1776 S32: 0.0369 S33: -0.0009 TLS GROUP : 2 SELECTION: chain 'A' and (resid 21 through 67 ) ORIGIN FOR THE GROUP (A): -9.8183 16.2082 -0.6115 T TENSOR T11: 0.1401 T22: 0.1135 T33: 0.1188 T12: -0.0136 T13: -0.0061 T23: 0.0202 L TENSOR L11: 0.1321 L22: 0.2349 L33: 0.2975 L12: 0.1778 L13: 0.0478 L23: 0.0941 S TENSOR S11: 0.0503 S12: -0.0614 S13: -0.1297 S21: 0.1592 S22: -0.0715 S23: 0.0082 S31: 0.1794 S32: -0.0393 S33: -0.0033 TLS GROUP : 3 SELECTION: chain 'A' and (resid 68 through 83 ) ORIGIN FOR THE GROUP (A): -3.3725 17.9002 4.8918 T TENSOR T11: 0.1653 T22: 0.1333 T33: 0.1106 T12: 0.0030 T13: -0.0335 T23: 0.0311 L TENSOR L11: 0.0103 L22: 0.0600 L33: 0.1330 L12: 0.0156 L13: 0.0350 L23: 0.0684 S TENSOR S11: 0.1033 S12: -0.1532 S13: -0.0980 S21: 0.1659 S22: -0.1020 S23: -0.0365 S31: 0.2602 S32: -0.0002 S33: -0.0018 TLS GROUP : 4 SELECTION: chain 'A' and (resid 84 through 105 ) ORIGIN FOR THE GROUP (A): -13.4106 25.0623 -6.4480 T TENSOR T11: 0.0853 T22: 0.1128 T33: 0.1023 T12: -0.0081 T13: -0.0063 T23: 0.0037 L TENSOR L11: 0.0229 L22: 0.0448 L33: 0.1506 L12: 0.0324 L13: 0.0273 L23: 0.0314 S TENSOR S11: 0.0258 S12: -0.0504 S13: 0.0126 S21: 0.0399 S22: -0.0105 S23: 0.0004 S31: 0.1612 S32: -0.0278 S33: 0.0017 TLS GROUP : 5 SELECTION: chain 'A' and (resid 106 through 277 ) ORIGIN FOR THE GROUP (A): -5.2108 26.0142 -16.7864 T TENSOR T11: 0.0709 T22: 0.0726 T33: 0.0796 T12: 0.0003 T13: -0.0075 T23: -0.0023 L TENSOR L11: 0.4987 L22: 0.4323 L33: 0.5287 L12: 0.0400 L13: 0.0130 L23: 0.1750 S TENSOR S11: -0.0104 S12: 0.0106 S13: -0.0222 S21: -0.0241 S22: 0.0181 S23: 0.0143 S31: 0.0254 S32: 0.0202 S33: -0.0299 TLS GROUP : 6 SELECTION: chain 'A' and (resid 278 through 305 ) ORIGIN FOR THE GROUP (A): -1.8368 5.1906 -14.6228 T TENSOR T11: 0.1762 T22: 0.0704 T33: 0.1738 T12: 0.0199 T13: -0.0341 T23: -0.0039 L TENSOR L11: 0.0612 L22: 0.0271 L33: 0.5427 L12: 0.0142 L13: -0.0876 L23: 0.0928 S TENSOR S11: -0.0322 S12: -0.0326 S13: -0.1932 S21: 0.1410 S22: 0.0170 S23: -0.0523 S31: 0.3172 S32: 0.0290 S33: -0.0064 TLS GROUP : 7 SELECTION: chain 'B' and (resid 1 through 20 ) ORIGIN FOR THE GROUP (A): -37.2340 18.7564 -34.5423 T TENSOR T11: 0.0942 T22: 0.1029 T33: 0.0882 T12: 0.0022 T13: 0.0050 T23: 0.0075 L TENSOR L11: 0.0418 L22: 0.0553 L33: 0.1267 L12: -0.0497 L13: 0.0541 L23: -0.0759 S TENSOR S11: -0.0385 S12: 0.0186 S13: -0.0736 S21: 0.0442 S22: -0.0057 S23: 0.0620 S31: 0.1486 S32: -0.0552 S33: -0.0010 TLS GROUP : 8 SELECTION: chain 'B' and (resid 21 through 52 ) ORIGIN FOR THE GROUP (A): -39.2103 14.5396 -41.5350 T TENSOR T11: 0.1233 T22: 0.1086 T33: 0.0965 T12: -0.0223 T13: -0.0020 T23: -0.0023 L TENSOR L11: 0.0747 L22: 0.1013 L33: 0.2624 L12: -0.0234 L13: 0.0824 L23: -0.1778 S TENSOR S11: -0.0064 S12: 0.0156 S13: -0.0650 S21: -0.0960 S22: 0.0248 S23: 0.0122 S31: 0.2164 S32: -0.0475 S33: 0.0090 TLS GROUP : 9 SELECTION: chain 'B' and (resid 53 through 105 ) ORIGIN FOR THE GROUP (A): -30.2180 24.3326 -44.3475 T TENSOR T11: 0.0705 T22: 0.1089 T33: 0.0822 T12: -0.0024 T13: -0.0009 T23: -0.0035 L TENSOR L11: 0.0954 L22: 0.2313 L33: 0.2848 L12: -0.1316 L13: -0.0106 L23: 0.0125 S TENSOR S11: 0.0033 S12: 0.0338 S13: -0.0161 S21: -0.0290 S22: 0.0035 S23: -0.0136 S31: 0.0737 S32: 0.0156 S33: -0.0004 TLS GROUP : 10 SELECTION: chain 'B' and (resid 106 through 171 ) ORIGIN FOR THE GROUP (A): -31.3265 33.6908 -38.1799 T TENSOR T11: 0.0655 T22: 0.0830 T33: 0.0830 T12: -0.0039 T13: -0.0065 T23: 0.0057 L TENSOR L11: 0.1059 L22: 0.2752 L33: 0.3056 L12: -0.0176 L13: -0.1524 L23: 0.0694 S TENSOR S11: -0.0066 S12: 0.0008 S13: 0.0146 S21: 0.0118 S22: 0.0262 S23: -0.0317 S31: -0.0156 S32: -0.0118 S33: 0.0395 TLS GROUP : 11 SELECTION: chain 'B' and (resid 172 through 231 ) ORIGIN FOR THE GROUP (A): -33.8116 28.5235 -20.9305 T TENSOR T11: 0.1134 T22: 0.0938 T33: 0.0816 T12: 0.0048 T13: 0.0040 T23: 0.0018 L TENSOR L11: 0.1423 L22: 0.2161 L33: 0.1880 L12: 0.1179 L13: -0.0485 L23: 0.1017 S TENSOR S11: -0.0003 S12: -0.0358 S13: -0.0055 S21: 0.1244 S22: -0.0047 S23: 0.0049 S31: -0.0047 S32: -0.0268 S33: -0.0010 TLS GROUP : 12 SELECTION: chain 'B' and (resid 232 through 246 ) ORIGIN FOR THE GROUP (A): -38.6467 24.5458 -23.8737 T TENSOR T11: 0.1195 T22: 0.0908 T33: 0.0854 T12: -0.0061 T13: 0.0146 T23: 0.0034 L TENSOR L11: 0.0309 L22: 0.0139 L33: 0.0773 L12: 0.0145 L13: 0.0160 L23: 0.0103 S TENSOR S11: 0.0318 S12: -0.0346 S13: -0.0006 S21: 0.1431 S22: -0.0635 S23: 0.0200 S31: 0.0447 S32: -0.0681 S33: -0.0010 TLS GROUP : 13 SELECTION: chain 'B' and (resid 247 through 262 ) ORIGIN FOR THE GROUP (A): -44.0834 18.9543 -16.0001 T TENSOR T11: 0.1571 T22: 0.1251 T33: 0.1047 T12: -0.0225 T13: 0.0258 T23: 0.0040 L TENSOR L11: 0.0251 L22: 0.0101 L33: 0.0163 L12: -0.0008 L13: -0.0037 L23: -0.0024 S TENSOR S11: 0.0299 S12: 0.0238 S13: -0.0133 S21: 0.1149 S22: -0.0420 S23: 0.0542 S31: 0.1603 S32: -0.1130 S33: 0.0004 TLS GROUP : 14 SELECTION: chain 'B' and (resid 263 through 305 ) ORIGIN FOR THE GROUP (A): -42.1993 13.5317 -28.3636 T TENSOR T11: 0.1267 T22: 0.1019 T33: 0.1003 T12: -0.0223 T13: 0.0003 T23: 0.0084 L TENSOR L11: 0.0446 L22: 0.1187 L33: 0.2422 L12: -0.0153 L13: -0.0015 L23: -0.1701 S TENSOR S11: 0.0116 S12: -0.0165 S13: -0.0261 S21: -0.0072 S22: 0.0175 S23: 0.0892 S31: 0.1343 S32: -0.0837 S33: 0.0267
RfactorNum. reflection% reflection
Rfree0.1591 9545 5 %
Rwork0.1487 --
obs0.1492 190872 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 9.77 Å2
Refinement stepCycle: LAST / Resolution: 1.18→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4743 0 63 743 5549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075345
X-RAY DIFFRACTIONf_angle_d1.0037418
X-RAY DIFFRACTIONf_dihedral_angle_d12.5122004
X-RAY DIFFRACTIONf_chiral_restr0.092805
X-RAY DIFFRACTIONf_plane_restr0.01970
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.18-1.190.28372960.2574563695
1.19-1.210.25413170.2426023100
1.21-1.220.24493160.23045985100
1.22-1.240.21353150.21585993100
1.24-1.250.22233170.20586024100
1.25-1.270.21523160.26006100
1.27-1.290.21293140.20055969100
1.29-1.310.19123140.19256028100
1.31-1.330.21893160.19096004100
1.33-1.350.19763160.18526012100
1.35-1.370.19723170.18246022100
1.37-1.40.20773170.18466015100
1.4-1.420.18563160.17426011100
1.42-1.450.1833170.15836019100
1.45-1.490.15613180.14496039100
1.49-1.520.14983160.13516008100
1.52-1.560.14263180.13036033100
1.56-1.60.14843180.12786053100
1.6-1.650.1433170.12676016100
1.65-1.70.13963190.136063100
1.7-1.760.1633190.12966057100
1.76-1.830.15763180.13756047100
1.83-1.920.15333200.13966065100
1.92-2.020.14633210.13756105100
2.02-2.140.14963190.13346071100
2.14-2.310.14633220.13756105100
2.31-2.540.15873210.14546107100
2.54-2.910.14753250.14396170100
2.91-3.660.14873270.13856211100
3.66-39.510.11943390.13016430100

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