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- PDB-7p12: DeNovoTIM13-SB, a de novo designed TIM barrel with a salt-bridge ... -

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Basic information

Entry
Database: PDB / ID: 7p12
TitleDeNovoTIM13-SB, a de novo designed TIM barrel with a salt-bridge cluster
ComponentsDeNovoTIM13-SB
KeywordsDE NOVO PROTEIN / TIM barrel / salt bridge cluster
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsKordes, S. / Romero-Romero, S. / Hocker, B.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO4022/2-3 Germany
European Research Council (ERC)ERC Consolidator grant 647548 Protein Lego Germany
CitationJournal: Protein Sci. / Year: 2022
Title: A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels.
Authors: Kordes, S. / Romero-Romero, S. / Lutz, L. / Hocker, B.
History
DepositionJul 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DeNovoTIM13-SB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2513
Polymers22,1211
Non-polymers1302
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-15 kcal/mol
Surface area8290 Å2
Unit cell
Length a, b, c (Å)39.400, 39.470, 39.400
Angle α, β, γ (deg.)113.320, 102.020, 113.297
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein DeNovoTIM13-SB


Mass: 22120.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: M (N-terminal) and LEHHHHHH (C-terminal) come from the expresion vector.
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: 0.17 M sodium acetate trihydrate, 0.085 M Tris pH8.9, 23% PEG 4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.69→32.65 Å / Num. obs: 20148 / % possible obs: 99.67 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.1995 / Rpim(I) all: 0.08262 / Rrim(I) all: 0.2165 / Net I/σ(I): 9.66
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.794 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 1981 / CC1/2: 0.596 / CC star: 0.864 / Rpim(I) all: 1.125 / Rrim(I) all: 3.016 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YQX

6yqx


Resolution: 1.69→32.65 Å / SU ML: 0.2881 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 43.0148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3147 1008 5 %
Rwork0.2655 19137 -
obs0.268 20145 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.05 Å2
Refinement stepCycle: LAST / Resolution: 1.69→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 6 21 1279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421263
X-RAY DIFFRACTIONf_angle_d0.68611723
X-RAY DIFFRACTIONf_chiral_restr0.0487224
X-RAY DIFFRACTIONf_plane_restr0.0041219
X-RAY DIFFRACTIONf_dihedral_angle_d4.7432189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.780.45591460.40592768X-RAY DIFFRACTION99.86
1.78-1.890.39991420.36552702X-RAY DIFFRACTION99.89
1.89-2.040.3481420.2972708X-RAY DIFFRACTION99.48
2.04-2.240.34361440.28082722X-RAY DIFFRACTION99.93
2.24-2.570.30071460.27292774X-RAY DIFFRACTION99.69
2.57-3.230.3551440.29862735X-RAY DIFFRACTION99.58
3.23-32.650.28891440.23892728X-RAY DIFFRACTION99.31
Refinement TLS params.Method: refined / Origin x: -10.9277169393 Å / Origin y: -2.74256954458 Å / Origin z: -14.2031739562 Å
111213212223313233
T0.209737253424 Å20.0702476283386 Å20.0130708871884 Å2-0.358057308674 Å20.0546938378124 Å2--0.258381702477 Å2
L4.95490936936 °21.16854365993 °2-2.43467870935 °2-4.66672800669 °21.35703968695 °2--4.58445900668 °2
S-0.055687780542 Å °-0.220765224752 Å °-0.0712476118753 Å °0.13907102439 Å °-0.00294950724347 Å °-0.307649302432 Å °0.150936316199 Å °0.167628548499 Å °0.0783253259606 Å °
Refinement TLS groupSelection details: all

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