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- PDB-6zv9: Terbium(III)-bound de novo TIM barrel-ferredoxin fold fusion dime... -

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Basic information

Entry
Database: PDB / ID: 6zv9
TitleTerbium(III)-bound de novo TIM barrel-ferredoxin fold fusion dimer with 4-glutamate binding site and tryptophan antenna (TFD-EE N6W)
ComponentsTFD-EE
KeywordsDE NOVO PROTEIN / Lanthanide-binding protein
Function / homologyRibosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / TERBIUM(III) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCaldwell, S. / Haydon, I. / Piperidou, N. / Huang, P. / Hilvert, D. / Baker, D. / Zeymer, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPZ00P2_179887 Switzerland
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
DepositionJul 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 9, 2020Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Dec 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 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,0354
Polymers37,8142
Non-polymers2212
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-34 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.970, 56.470, 71.280
Angle α, β, γ (deg.)90.000, 101.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TFD-EE


Mass: 18906.947 Da / Num. of mol.: 2 / Mutation: N6W
Source method: isolated from a genetically manipulated source
Details: The first four amino acids (GAMG) are not part of the de novo designed sequence, but a results of the cloning and purification strategy. They are thus numbered -3, -2, -1, 0.
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M HEPES pH 7.5, 20 % PEG 4000, and 10 % iso-propanol, containing Gly3 as an additive

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 56427 / % possible obs: 98.4 % / Redundancy: 3.06 % / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 13.12
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.97 % / Mean I/σ(I) obs: 1.94 / Num. unique obs: 8189 / CC1/2: 0.845 / Rrim(I) all: 0.697 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Single domain Rosetta models

Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.792 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1463 5 %RANDOM
Rwork0.1949 ---
obs0.1958 27802 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.69 Å2 / Biso mean: 47.312 Å2 / Biso min: 22.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å20.92 Å2
2---3.53 Å2-0 Å2
3---3.14 Å2
Refinement stepCycle: final / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 5 44 2644
Biso mean--30.28 42.83 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132622
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172669
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.6283519
X-RAY DIFFRACTIONr_angle_other_deg1.11.5896171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.38723.083133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03215537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2771520
X-RAY DIFFRACTIONr_chiral_restr0.0380.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_rigid_bond_restr0.73935291
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 108 -
Rwork0.318 2048 -
all-2156 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0962-0.0189-0.02410.08880.05670.0432-0.00540.03520.0137-0.00270.00630.00280.00960.014-0.00080.0523-0.0004-0.00820.07880.00730.005823.7004-13.326819.0687
20.3425-0.1018-0.05680.05340.05120.06190.00330.0566-0.01680.0121-0.02860.01910.0134-0.01880.02530.0550.0001-0.00290.0817-0.0020.0136.6976-12.104817.1349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 166
2X-RAY DIFFRACTION2B0 - 168

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