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- PDB-7ot7: sTIM11noCys-SB, a de novo designed TIM barrel with a salt-bridge ... -

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Basic information

Entry
Database: PDB / ID: 7ot7
TitlesTIM11noCys-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 2)
ComponentssTIM11noCys-SB
KeywordsDE NOVO PROTEIN / TIM barrel / salt bridge cluster
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsRomero-Romero, S. / Kordes, 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: sTIM11noCys-SB


Theoretical massNumber of molelcules
Total (without water)22,9781
Polymers22,9781
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.695, 50.695, 132.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-244-

HOH

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Components

#1: Protein sTIM11noCys-SB


Mass: 22977.523 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 34% PEG 400, 0.1 M Tris pH7.78, 0.2 M LiSO4

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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: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.51→47.33 Å / Num. obs: 27801 / % possible obs: 99.87 % / Redundancy: 13.8 % / Biso Wilson estimate: 28.67 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0596 / Rpim(I) all: 0.017 / Rrim(I) all: 0.0619 / Net I/σ(I): 18.9
Reflection shellResolution: 1.51→1.57 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 2677 / CC1/2: 0.425 / CC star: 0.772 / Rpim(I) all: 0.683 / Rrim(I) all: 2.35 / % possible all: 99.04

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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: 1.51→47.33 Å / SU ML: 0.2068 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0311
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 1390 5 %
Rwork0.2159 26396 -
obs0.2174 27786 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.84 Å2
Refinement stepCycle: LAST / Resolution: 1.51→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 0 82 1498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011458
X-RAY DIFFRACTIONf_angle_d0.99961988
X-RAY DIFFRACTIONf_chiral_restr0.0575216
X-RAY DIFFRACTIONf_plane_restr0.0092258
X-RAY DIFFRACTIONf_dihedral_angle_d5.8185203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.570.36251340.34832541X-RAY DIFFRACTION99
1.57-1.630.34241370.2932603X-RAY DIFFRACTION99.93
1.63-1.70.33411360.25542590X-RAY DIFFRACTION100
1.7-1.790.28711370.26532595X-RAY DIFFRACTION99.96
1.79-1.910.30981360.25292590X-RAY DIFFRACTION99.93
1.91-2.050.26161380.21722627X-RAY DIFFRACTION99.82
2.05-2.260.23741390.2042623X-RAY DIFFRACTION100
2.26-2.590.25271390.20862659X-RAY DIFFRACTION100
2.59-3.260.2361420.22652697X-RAY DIFFRACTION100
3.26-47.330.22841520.19992871X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.7751386333 Å / Origin y: 7.57193852469 Å / Origin z: 4.94351960703 Å
111213212223313233
T0.161750579666 Å2-0.0312163953639 Å20.0277939373286 Å2-0.153476612324 Å2-0.0630611900585 Å2--0.173084681556 Å2
L4.58818869617 °20.0854803101103 °2-1.22234489941 °2-1.61368663278 °2-0.436058059392 °2--1.98918738864 °2
S-0.0430879819123 Å °-0.332303006605 Å °0.069957334115 Å °0.0884962843007 Å °0.0474183942089 Å °0.0281326317949 Å °-0.0904771640092 Å °-0.0395628507229 Å °0.0140427001804 Å °
Refinement TLS groupSelection details: all

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