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- PDB-8q28: Se-Met labelled TtX122A - A domain of unknown function from the T... -

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Basic information

Entry
Database: PDB / ID: 8q28
TitleSe-Met labelled TtX122A - A domain of unknown function from the Teredinibacter turnerae protein TERTU_3803
ComponentsGluconolactonase domain protein
KeywordsUNKNOWN FUNCTION / beta-jelly roll fold / X122 / CAZy / Teredinibacter turnerae
Function / homology
Function and homology information


cellulose binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Domain of unknown function DUF1587 / Domain of unknown function DUF1588 / Domain of unknown function DUF1592 / Domain of unknown function DUF1595 / Protein of unknown function (DUF1587) / Protein of unknown function (DUF1588) / Protein of unknown function (DUF1592) / Protein of unknown function (DUF1595) / Carbohydrate binding module family 10 / CBM10 superfamily ...Domain of unknown function DUF1587 / Domain of unknown function DUF1588 / Domain of unknown function DUF1592 / Domain of unknown function DUF1595 / Protein of unknown function (DUF1587) / Protein of unknown function (DUF1588) / Protein of unknown function (DUF1592) / Protein of unknown function (DUF1595) / Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Senescence marker protein-30 (SMP-30) / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Soluble quinoprotein glucose/sorbosone dehydrogenase / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / NHL repeat profile. / NHL repeat / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Cytochrome C oxidase, cbb3-type, subunit III / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-bladed beta-propeller, TolB-like / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Gluconolactonase domain protein
Similarity search - Component
Biological speciesTeredinibacter turnerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsRajagopal, B.S. / Hemsworth, G.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N019970/1 United Kingdom
CitationJournal: Iucrj / Year: 2024
Title: Structural dissection of two redox proteins from the shipworm symbiont Teredinibacter turnerae.
Authors: Rajagopal, B.S. / Yates, N. / Smith, J. / Paradisi, A. / Tetard-Jones, C. / Willats, W.G.T. / Marcus, S. / Knox, J.P. / Firdaus-Raih, M. / Henrissat, B. / Davies, G.J. / Walton, P.H. / ...Authors: Rajagopal, B.S. / Yates, N. / Smith, J. / Paradisi, A. / Tetard-Jones, C. / Willats, W.G.T. / Marcus, S. / Knox, J.P. / Firdaus-Raih, M. / Henrissat, B. / Davies, G.J. / Walton, P.H. / Parkin, A. / Hemsworth, G.R.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 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

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Assembly

Deposited unit
A: Gluconolactonase domain protein
B: Gluconolactonase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,79812
Polymers55,3732
Non-polymers42610
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.004, 75.443, 69.751
Angle α, β, γ (deg.)90.000, 107.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gluconolactonase domain protein


Mass: 27686.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Teredinibacter turnerae (bacteria) / Gene: TERTU_3803 / Production host: Escherichia coli (E. coli) / References: UniProt: C5BSV8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.1 M magnesium acetate, 15-25% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97982, 0.98000, 0.96450
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979821
20.981
30.96451
ReflectionResolution: 1.8→49.88 Å / Num. obs: 43829 / % possible obs: 99.6 % / Redundancy: 6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.065 / Rrim(I) all: 0.111 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-49.885.60.0473780.9950.0350.059
1.8-1.844.30.27825080.9120.2320.364

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
SHELXphasing
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→49.88 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.497 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2022 2157 4.924 %
Rwork0.1569 41651 -
all0.159 --
obs-43808 99.53 %
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: 19.913 Å2
Baniso -1Baniso -2Baniso -3
1-0.273 Å2-0 Å21.425 Å2
2---0.796 Å2-0 Å2
3----0.318 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 22 391 4162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0123885
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163387
X-RAY DIFFRACTIONr_angle_refined_deg2.1191.6465289
X-RAY DIFFRACTIONr_angle_other_deg0.7441.5947778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4445485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.536512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4810538
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.40610216
X-RAY DIFFRACTIONr_chiral_restr0.1130.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02969
X-RAY DIFFRACTIONr_nbd_refined0.2080.2678
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.23293
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21864
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.22060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2333
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1060.28
X-RAY DIFFRACTIONr_nbd_other0.2210.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.215
X-RAY DIFFRACTIONr_mcbond_it2.8112.0481928
X-RAY DIFFRACTIONr_mcbond_other2.7452.0471928
X-RAY DIFFRACTIONr_mcangle_it3.4723.6662408
X-RAY DIFFRACTIONr_mcangle_other3.4723.6672409
X-RAY DIFFRACTIONr_scbond_it3.4572.2281957
X-RAY DIFFRACTIONr_scbond_other3.4572.2281958
X-RAY DIFFRACTIONr_scangle_it4.7173.9812878
X-RAY DIFFRACTIONr_scangle_other4.7163.9812879
X-RAY DIFFRACTIONr_lrange_it6.00921.8684334
X-RAY DIFFRACTIONr_lrange_other6.00921.8684334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2631610.1982980X-RAY DIFFRACTION96.2021
1.847-1.8970.2321710.1672939X-RAY DIFFRACTION99.9679
1.897-1.9520.2151510.1632921X-RAY DIFFRACTION100
1.952-2.0120.2331410.1732847X-RAY DIFFRACTION99.8997
2.012-2.0780.2081680.1632733X-RAY DIFFRACTION99.9311
2.078-2.1510.221290.1592622X-RAY DIFFRACTION99.8911
2.151-2.2320.1961370.1532598X-RAY DIFFRACTION99.9269
2.232-2.3230.2011220.1462469X-RAY DIFFRACTION99.8459
2.323-2.4260.2151320.1542358X-RAY DIFFRACTION99.9599
2.426-2.5440.2171220.1542268X-RAY DIFFRACTION99.7496
2.544-2.6810.232920.1532173X-RAY DIFFRACTION99.6042
2.681-2.8430.217960.1512027X-RAY DIFFRACTION99.6714
2.843-3.0390.1971090.1531925X-RAY DIFFRACTION99.8037
3.039-3.2810.2031010.1641770X-RAY DIFFRACTION99.7335
3.281-3.5930.212820.1641674X-RAY DIFFRACTION99.8294
3.593-4.0140.195740.1591492X-RAY DIFFRACTION99.8088
4.014-4.6310.135580.131322X-RAY DIFFRACTION99.3521
4.631-5.6590.133380.1371136X-RAY DIFFRACTION99.3232
5.659-7.9520.181480.161889X-RAY DIFFRACTION99.787
7.952-49.880.156250.183508X-RAY DIFFRACTION99.8127

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