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- PDB-6wxo: De novo TIM barrel-ferredoxin fold fusion homodimer with 2-histid... -

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Basic information

Entry
Database: PDB / ID: 6wxo
TitleDe novo TIM barrel-ferredoxin fold fusion homodimer with 2-histidine 2-glutamate centre TFD-HE
ComponentsTFD-HE
KeywordsDE NOVO PROTEIN / TIM barrel / ferredoxin fold / homodimer / symmetric fusion / hyperstable / symmetric / de novo / repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsCaldwell, S.J. / Zeymer, C. / Haydon, I.C. / Huang, P. / Hilvert, D. / Baker, D.
Funding support United States, Tajikistan, 2items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-19-1-0003 United States
Swiss National Science FoundationTajikistan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion.
Authors: Caldwell, S.J. / Haydon, I.C. / Piperidou, N. / Huang, P.S. / Bick, M.J. / Sjostrom, H.S. / Hilvert, D. / Baker, D. / Zeymer, C.
History
DepositionMay 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Advisory / Database references
Category: citation / citation_author / pdbx_validate_close_contact
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TFD-HE
B: TFD-HE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4056
Polymers42,0242
Non-polymers3804
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Rosetta - designed homodimer, runs on SEC the same as a fused monomer containing twice the protein in a single chain.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-58 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.851, 62.512, 48.949
Angle α, β, γ (deg.)90.000, 95.269, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and (resid -5 or (resid -4 through -2...
d_2ens_1(chain "A" and (resid -5 through 14 or resid 16...
d_1ens_2(chain "A" and (resid -5 through 14 or resid 16...
d_2ens_2(chain "B" and (resid -5 or (resid -4 through -2...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEULYSA11 - 30
d_12ens_1VALSERA32 - 47
d_13ens_1ASPTHRA49 - 74
d_14ens_1ARGGLUA78 - 91
d_15ens_1ILEILEA95 - 116
d_16ens_1ILEGLUA118 - 154
d_17ens_1LEUARGA158 - 165
d_18ens_1LEULEUA167 - 186
d_21ens_1LEULYSB1 - 20
d_22ens_1VALSERB24 - 39
d_23ens_1ASPTHRB43 - 68
d_24ens_1ARGGLUB70 - 83
d_25ens_1ILEILEB87 - 108
d_26ens_1ILEGLUB112 - 148
d_27ens_1LEUARGB152 - 159
d_28ens_1LEULEUB163 - 182
d_11ens_2LEULYSB1 - 20
d_12ens_2VALSERB24 - 39
d_13ens_2ASPTHRB43 - 68
d_14ens_2ARGGLUB70 - 83
d_15ens_2ILEILEB87 - 108
d_16ens_2ILEGLUB112 - 148
d_17ens_2LEUARGB152 - 159
d_18ens_2LEULEUB163 - 182
d_21ens_2LEULYSA11 - 30
d_22ens_2VALSERA32 - 47
d_23ens_2ASPTHRA49 - 74
d_24ens_2ARGGLUA78 - 91
d_25ens_2ILEILEA95 - 116
d_26ens_2ILEGLUA118 - 154
d_27ens_2LEUARGA158 - 165
d_28ens_2LEULEUA167 - 186

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein TFD-HE


Mass: 21012.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.77 Å3/Da / Density % sol: 30.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Citric Acid pH 4.0 and 2.4 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→32.95 Å / Num. obs: 56179 / % possible obs: 97.05 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.91 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1051 / Rpim(I) all: 0.0614 / Rrim(I) all: 0.1221 / Net I/σ(I): 7.25
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.87 / Mean I/σ(I) obs: 0.71 / Num. unique obs: 5536 / CC1/2: 0.192 / CC star: 0.567 / Rpim(I) all: 1.099 / Rrim(I) all: 2.177 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TIM barrel component of Rosetta model of TFD-HE.

Resolution: 1.41→32.95 Å / SU ML: 0.2096 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2121 1179 2.15 %
Rwork0.1827 53711 -
obs0.1833 54890 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.29 Å2
Refinement stepCycle: LAST / Resolution: 1.41→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 21 168 2804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242698
X-RAY DIFFRACTIONf_angle_d1.09563638
X-RAY DIFFRACTIONf_chiral_restr0.0846438
X-RAY DIFFRACTIONf_plane_restr0.0069462
X-RAY DIFFRACTIONf_dihedral_angle_d17.91811004
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.17450278897
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.17450278897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.470.35581410.33826592X-RAY DIFFRACTION95.22
1.47-1.550.37521490.31056612X-RAY DIFFRACTION96.39
1.55-1.650.30821490.22666750X-RAY DIFFRACTION97.86
1.65-1.780.25021520.19026783X-RAY DIFFRACTION98.49
1.78-1.960.25641450.17156719X-RAY DIFFRACTION97.13
1.96-2.240.18571460.1486697X-RAY DIFFRACTION97.05
2.24-2.820.17591470.17016871X-RAY DIFFRACTION98.91
2.82-32.950.18421500.17166687X-RAY DIFFRACTION95.25

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