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- PDB-8pof: The crystal structure of RsSymEG1 reveals a unique form of smalle... -

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Basic information

Entry
Database: PDB / ID: 8pof
TitleThe crystal structure of RsSymEG1 reveals a unique form of smaller GH7 endoglucanases alongside GH7 cellobiohydrolases in protist symbionts of termites
ComponentsPutative glycosyl hydrolase family7
KeywordsHYDROLASE / GH7 / endoglucanase / cellulase
Function / homologyGlycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / cellulase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / cellulase
Function and homology information
Biological speciesReticulitermes speratus gut symbiotic protist (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHaataja, T. / Sandgren, M. / Hansson, H. / Stahlberg, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Energy Agency2015-009633 Sweden
CitationJournal: Febs J. / Year: 2024
Title: The crystal structure of RsSymEG1 reveals a unique form of smaller GH7 endoglucanases alongside GH7 cellobiohydrolases in protist symbionts of termites.
Authors: Haataja, T. / Hansson, H. / Moriya, S. / Sandgren, M. / Stahlberg, J.
History
DepositionJul 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 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: Putative glycosyl hydrolase family7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1003
Polymers33,9541
Non-polymers1452
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-5 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.604, 114.604, 49.963
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-624-

HOH

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Components

#1: Protein Putative glycosyl hydrolase family7


Mass: 33954.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reticulitermes speratus gut symbiotic protist (eukaryote)
Production host: Aspergillus oryzae (mold) / References: UniProt: A4UWN6
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.03 M Sodium fluoride, 0.03 M Sodium bromide, 0.03 M Sodium iodide, 12% v/v PEG 500 MME, 6 % w/v PEG 20000, 0.1 M Tris-Bicine pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 21, 2021 / Details: KB mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→45.8 Å / Num. obs: 27804 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.996 / Net I/σ(I): 9.8
Reflection shellResolution: 1.85→1.89 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1666 / CC1/2: 0.821

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→45.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1866 1405 5.055 %
Rwork0.1659 26388 -
all0.167 --
obs-27793 99.731 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.228 Å2-0 Å2-0 Å2
2---0.228 Å20 Å2
3---0.457 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 9 203 2589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132480
X-RAY DIFFRACTIONr_bond_other_d0.0370.0152242
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.6453381
X-RAY DIFFRACTIONr_angle_other_deg2.4041.5875182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2185333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24624.018112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17315384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.061510
X-RAY DIFFRACTIONr_chiral_restr0.050.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022930
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02550
X-RAY DIFFRACTIONr_nbd_refined0.1890.2426
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.22063
X-RAY DIFFRACTIONr_nbtor_refined0.1490.21214
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.21079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2193
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.214
X-RAY DIFFRACTIONr_nbd_other0.1880.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.214
X-RAY DIFFRACTIONr_mcbond_it0.9262.1191318
X-RAY DIFFRACTIONr_mcbond_other0.9242.1181316
X-RAY DIFFRACTIONr_mcangle_it1.483.1721652
X-RAY DIFFRACTIONr_mcangle_other1.4813.1721653
X-RAY DIFFRACTIONr_scbond_it1.372.2131162
X-RAY DIFFRACTIONr_scbond_other1.372.2141163
X-RAY DIFFRACTIONr_scangle_it2.2063.2591728
X-RAY DIFFRACTIONr_scangle_other2.2053.2591729
X-RAY DIFFRACTIONr_lrange_it3.6225.2152755
X-RAY DIFFRACTIONr_lrange_other3.50824.9732724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.257850.211902X-RAY DIFFRACTION98.9542
1.898-1.950.193940.1921901X-RAY DIFFRACTION99.8998
1.95-2.0060.1941010.1791867X-RAY DIFFRACTION99.8985
2.006-2.0680.227960.1721763X-RAY DIFFRACTION99.8925
2.068-2.1360.197880.1591736X-RAY DIFFRACTION100
2.136-2.210.188940.1581671X-RAY DIFFRACTION99.9434
2.21-2.2940.1751040.1521629X-RAY DIFFRACTION100
2.294-2.3870.146820.1411543X-RAY DIFFRACTION99.9385
2.387-2.4930.168940.1431500X-RAY DIFFRACTION99.9373
2.493-2.6140.162700.1511430X-RAY DIFFRACTION99.8004
2.614-2.7550.187900.1541337X-RAY DIFFRACTION99.86
2.755-2.9220.195650.1641302X-RAY DIFFRACTION99.563
2.922-3.1220.186670.1711207X-RAY DIFFRACTION99.7651
3.122-3.3710.18520.1611149X-RAY DIFFRACTION99.8337
3.371-3.6910.206610.1631036X-RAY DIFFRACTION99.5463
3.691-4.1230.159410.163954X-RAY DIFFRACTION99.5996
4.123-4.7550.204470.158830X-RAY DIFFRACTION98.9842
4.755-5.8080.162290.179731X-RAY DIFFRACTION99.8686
5.808-8.1480.202270.207570X-RAY DIFFRACTION99.6661
8.148-45.80.204180.193330X-RAY DIFFRACTION98.3051

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