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- PDB-7osv: DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge c... -

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Basic information

Entry
Database: PDB / ID: 7osv
TitleDeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)
ComponentsDeNovoTIM6-SB
KeywordsDE NOVO PROTEIN / TIM barrel / salt bridge cluster
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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
DepositionJun 9, 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: DeNovoTIM6-SB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9905
Polymers22,6701
Non-polymers3204
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint0 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.370, 65.630, 44.610
Angle α, β, γ (deg.)90.000, 95.738, 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

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Components

#1: Protein DeNovoTIM6-SB


Mass: 22669.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: M (N-terminal) and GLEHHHHHH (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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M Ammonium sulfate, 0.2 M sodium acetate pH 4.6, 28% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→32.81 Å / Num. obs: 19751 / % possible obs: 98.89 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.41 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1385 / Rpim(I) all: 0.057 / Rrim(I) all: 0.1501 / Net I/σ(I): 7.77
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 7 % / Rmerge(I) obs: 1.77 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 1947 / CC1/2: 0.339 / CC star: 0.712 / Rpim(I) all: 1.114 / Rrim(I) all: 2.99 / % possible all: 97.45

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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: 5BVL

5bvl


Resolution: 1.66→32.81 Å / SU ML: 0.2675 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 988 5 %
Rwork0.2088 18763 -
obs0.2102 19751 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.7 Å2
Refinement stepCycle: LAST / Resolution: 1.66→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 20 116 1490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571390
X-RAY DIFFRACTIONf_angle_d0.59151876
X-RAY DIFFRACTIONf_chiral_restr0.0492212
X-RAY DIFFRACTIONf_plane_restr0.0049244
X-RAY DIFFRACTIONf_dihedral_angle_d6.9304196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.750.37131370.37672596X-RAY DIFFRACTION96.47
1.75-1.850.31511410.2992685X-RAY DIFFRACTION99.37
1.85-20.30671400.25212672X-RAY DIFFRACTION98.77
2-2.20.22041400.19732664X-RAY DIFFRACTION98.08
2.2-2.520.23951430.19272700X-RAY DIFFRACTION99.61
2.52-3.170.23661430.21282727X-RAY DIFFRACTION99.86
3.17-32.810.21311440.18652719X-RAY DIFFRACTION98.55
Refinement TLS params.Method: refined / Origin x: 17.9931368244 Å / Origin y: 23.1375605104 Å / Origin z: 32.2013283573 Å
111213212223313233
T0.212796659671 Å20.00521804960816 Å2-0.0202153947368 Å2-0.216594015614 Å2-0.00283005543353 Å2--0.239535023311 Å2
L1.30125327439 °2-0.250492565247 °2-0.325710612097 °2-2.21671224645 °20.0699320893767 °2--0.530300339686 °2
S0.0310699388861 Å °0.0229723508743 Å °0.0207181176714 Å °0.0718513497851 Å °-0.0372212397213 Å °-0.00679287723548 Å °-0.0257536964751 Å °-0.0434031719452 Å °0.019597622216 Å °
Refinement TLS groupSelection details: all

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