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- PDB-7ot8: DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge c... -

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Entry
Database: PDB / ID: 7ot8
TitleDeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 2)
ComponentsDeNovoTIM6-SB
KeywordsDE NOVO PROTEIN / TIM barrel / salt bridge cluster
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
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
B: DeNovoTIM6-SB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5324
Polymers45,3392
Non-polymers1922
Water88349
1
A: DeNovoTIM6-SB


Theoretical massNumber of molelcules
Total (without water)22,6701
Polymers22,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DeNovoTIM6-SB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8623
Polymers22,6701
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.862, 74.899, 155.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein DeNovoTIM6-SB


Mass: 22669.711 Da / Num. of mol.: 2
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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 0.2 M Ammonium sulfate, 0.2 M sodium acetate pH 4.3, 31% PEG4000

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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: 2.22→42.56 Å / Num. obs: 22258 / % possible obs: 98.38 % / Redundancy: 13.1 % / Biso Wilson estimate: 47.03 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1409 / Rpim(I) all: 0.041 / Rrim(I) all: 0.1471 / Net I/σ(I): 10.9
Reflection shellResolution: 2.22→2.31 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 2081 / CC1/2: 0.464 / CC star: 0.796 / Rpim(I) all: 0.606 / Rrim(I) all: 2.26 / % possible all: 94.97

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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: 2.22→42.56 Å / SU ML: 0.4223 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.1931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3233 1066 4.8 %
Rwork0.2708 21131 -
obs0.2734 22197 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.37 Å2
Refinement stepCycle: LAST / Resolution: 2.22→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2537 0 10 49 2596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212584
X-RAY DIFFRACTIONf_angle_d0.40123526
X-RAY DIFFRACTIONf_chiral_restr0.0416422
X-RAY DIFFRACTIONf_plane_restr0.0022444
X-RAY DIFFRACTIONf_dihedral_angle_d5.4116364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.320.42181190.36182511X-RAY DIFFRACTION95.78
2.32-2.450.34921140.34212591X-RAY DIFFRACTION98.69
2.45-2.60.39911350.33632620X-RAY DIFFRACTION98.71
2.6-2.80.49021290.36582624X-RAY DIFFRACTION98.71
2.8-3.080.3371410.31462621X-RAY DIFFRACTION98.61
3.08-3.530.32271280.28822665X-RAY DIFFRACTION99.18
3.53-4.440.29071460.22182667X-RAY DIFFRACTION98.43
4.44-42.560.28991540.23542832X-RAY DIFFRACTION99.04
Refinement TLS params.Method: refined / Origin x: -20.4203584119 Å / Origin y: -19.0455689419 Å / Origin z: -1.71533611234 Å
111213212223313233
T0.351505175709 Å20.00243251089081 Å20.0911052127641 Å2-0.32146489169 Å20.00510279552473 Å2--0.446586942038 Å2
L0.793269421363 °20.0431406786836 °21.18568101028 °2-1.21924200963 °2-0.0488803198815 °2--2.6041980894 °2
S-0.0252295129977 Å °0.0222037513954 Å °-0.0762723952807 Å °0.0736185716494 Å °0.000653011392092 Å °-0.0245033352463 Å °0.149661993466 Å °0.0267771864201 Å °0.0182090413915 Å °
Refinement TLS groupSelection details: all

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