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- PDB-8anx: E329A Mutant Thermogutta terrifontis endoglucanase catalytic doma... -

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Basic information

Entry
Database: PDB / ID: 8anx
TitleE329A Mutant Thermogutta terrifontis endoglucanase catalytic domain with C-linker from glycoside hydrolase family 5 (TtEnd5A-CDC-E329A)
ComponentsEndoglucanase
KeywordsHYDROLASE / endoglucanase / endocellulase / inactive mutant
Function / homology
Function and homology information


cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesThermogutta terrifontis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHussain, N. / Mikolajek, H. / Naismith, J.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Commonwealth Scholarship Commission (United Kingdom)PKCN-2019-176 United Kingdom
Wellcome Trust100209/Z/12/Z United Kingdom
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Structural and functional snapshots of a broad-specificity endoglucanase from Thermogutta terrifontis for biomass saccharification.
Authors: Hussain, N. / Mikolajek, H. / Harrison, P.J. / Paterson, N. / Akhtar, M.W. / Sadaf, S. / Naismith, J.H.
History
DepositionAug 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)39,8321
Polymers39,8321
Non-polymers00
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13790 Å2
Unit cell
Length a, b, c (Å)60.390, 69.590, 81.920
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 Endoglucanase


Mass: 39831.727 Da / Num. of mol.: 1 / Mutation: E329A
Source method: isolated from a genetically manipulated source
Details: TtEnd5A-CDC-E329A is an inactive mutant of TtEnd5A-CD, in which glutamic acid (E329) has been mutated with alanine (329A). TtEnd5A-CDC itself a truncated variant of our previously deposited ...Details: TtEnd5A-CDC-E329A is an inactive mutant of TtEnd5A-CD, in which glutamic acid (E329) has been mutated with alanine (329A). TtEnd5A-CDC itself a truncated variant of our previously deposited Thermogutta terrifontis endoglucanase from glycoside hydrolase family 5 (TtEnd5A). TtEnd5A-CDC-E329A is comprised of a catalytic domain and a linker at C-terminal (186-531 amino caids).
Source: (gene. exp.) Thermogutta terrifontis (bacteria) / Gene: THTE_1171 / Plasmid: pEHISTEV vector
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / Variant (production host): OverExpress C43(DE3) / References: UniProt: A0A286RCT9, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M NH4Cl and 20%W/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.13→69.59 Å / Num. obs: 125321 / % possible obs: 96.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 13.69 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.013 / Rrim(I) all: 0.047 / Χ2: 0.94 / Net I/σ(I): 18.9
Reflection shellResolution: 1.13→1.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.646 / Num. unique obs: 7072 / CC1/2: 0.392 / Χ2: 0.83 / % possible all: 75.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AG9

8ag9


Resolution: 1.2→69.59 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.958 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1484 5308 4.913 %
Rwork0.1199 102734 -
all0.121 --
obs-108042 99.712 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.638 Å2
Baniso -1Baniso -2Baniso -3
1--0.468 Å20 Å2-0 Å2
2---0.339 Å20 Å2
3---0.808 Å2
Refinement stepCycle: LAST / Resolution: 1.2→69.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 0 375 3094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132896
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172574
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.6393975
X-RAY DIFFRACTIONr_angle_other_deg1.51.5765964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24521.297185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81515446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6531527
X-RAY DIFFRACTIONr_chiral_restr0.0750.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02689
X-RAY DIFFRACTIONr_nbd_refined0.2240.2573
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.22470
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21384
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21241
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1390.216
X-RAY DIFFRACTIONr_nbd_other0.1960.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4410.258
X-RAY DIFFRACTIONr_mcbond_it1.0041.4981363
X-RAY DIFFRACTIONr_mcbond_other0.9991.4951362
X-RAY DIFFRACTIONr_mcangle_it1.3532.2581709
X-RAY DIFFRACTIONr_mcangle_other1.3542.261710
X-RAY DIFFRACTIONr_scbond_it1.5711.7541533
X-RAY DIFFRACTIONr_scbond_other1.5691.7531533
X-RAY DIFFRACTIONr_scangle_it1.9452.5452252
X-RAY DIFFRACTIONr_scangle_other1.9472.5482253
X-RAY DIFFRACTIONr_lrange_it2.67118.813449
X-RAY DIFFRACTIONr_lrange_other2.33617.9843357
X-RAY DIFFRACTIONr_rigid_bond_restr1.1935470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.2-1.2310.2593740.24772450.24879060.8420.85196.36980.227
1.231-1.2650.2274150.19773140.19977450.9040.91299.79340.172
1.265-1.3020.1773510.16271530.16275050.9410.94499.98670.137
1.302-1.3420.1713390.13470130.13673520.9520.961000.111
1.342-1.3860.1423400.11567010.11670410.9670.9731000.093
1.386-1.4340.1523640.10765340.10968990.9670.97799.98550.087
1.434-1.4880.1313050.09663010.09766060.9770.9831000.078
1.488-1.5490.1282850.08461080.08563930.9810.9861000.07
1.549-1.6180.1222860.0858490.08261350.9820.9881000.068
1.618-1.6970.1182980.0855610.08258590.9840.9891000.07
1.697-1.7890.113060.0852870.08155930.9860.991000.071
1.789-1.8970.1152480.08850610.08953090.9850.9881000.081
1.897-2.0280.1182610.147240.10149850.9840.9861000.094
2.028-2.190.1332420.11244080.11346500.9790.9841000.109
2.19-2.3990.142080.10841010.10943090.9770.9831000.108
2.399-2.6820.1321750.11537350.11639100.9810.9831000.121
2.682-3.0960.1421720.12432970.12534690.9780.9811000.135
3.096-3.790.1541370.12828220.12929590.9750.9811000.147
3.79-5.3510.1751220.13822190.1423420.9770.9899.95730.17
5.351-69.590.215770.19812850.19913660.970.97299.70720.238

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