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

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Basic information

Entry
Database: PDB / ID: 7osu
TitlesTIM11noCys-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)
ComponentssTIM11noCys-SB
KeywordsDE NOVO PROTEIN / TIM barrel / salt bridge cluster
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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
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

Downloads & links

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Assembly

Deposited unit
A: sTIM11noCys-SB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2114
Polymers22,9781
Non-polymers2343
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-5 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.720, 50.720, 131.090
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-363-

HOH

21A-388-

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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50% PEG 200, 0.2 M NaCl, 0.1 M Phosphate citrate pH5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9874 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: 0.9874 Å / Relative weight: 1
ReflectionResolution: 1.37→47.3 Å / Num. obs: 36942 / % possible obs: 99.92 % / Redundancy: 14.1 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.024 / Rrim(I) all: 0.0904 / Net I/σ(I): 13.3
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.04 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3614 / CC1/2: 0.66 / CC star: 0.884 / Rpim(I) all: 0.558 / Rrim(I) all: 2.11 / % possible all: 99.92

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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: 1.37→47.3 Å / SU ML: 0.1837 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1336
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 1848 5 %
Rwork0.2086 35094 -
obs0.2106 36942 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.64 Å2
Refinement stepCycle: LAST / Resolution: 1.37→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 14 97 1553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541527
X-RAY DIFFRACTIONf_angle_d0.73942075
X-RAY DIFFRACTIONf_chiral_restr0.0712221
X-RAY DIFFRACTIONf_plane_restr0.0057268
X-RAY DIFFRACTIONf_dihedral_angle_d5.8645218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.410.34691390.37532644X-RAY DIFFRACTION99.54
1.41-1.450.36011380.33312623X-RAY DIFFRACTION99.78
1.45-1.490.28711420.26752683X-RAY DIFFRACTION100
1.49-1.550.27821370.24452605X-RAY DIFFRACTION99.85
1.55-1.610.27641390.23612645X-RAY DIFFRACTION99.86
1.61-1.680.26681410.22362679X-RAY DIFFRACTION99.86
1.68-1.770.28761410.24282667X-RAY DIFFRACTION99.93
1.77-1.880.26561420.22822708X-RAY DIFFRACTION99.96
1.88-2.030.24961410.20292682X-RAY DIFFRACTION99.96
2.03-2.230.21621430.19092704X-RAY DIFFRACTION99.96
2.23-2.560.25581440.19912740X-RAY DIFFRACTION99.97
2.56-3.220.22011450.21562760X-RAY DIFFRACTION100
3.22-47.30.24911560.19462954X-RAY DIFFRACTION100
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)
15.45388708779-2.82763120688-2.939338150418.571709550355.880050104169.80606750066-0.298838871923-1.18342107843-0.637921829281.575332210340.713268542816-0.4463882054361.121392456740.456102060766-0.388042941070.6457648289270.0101560821635-0.04675254263570.6895210068830.07659739236720.519752053077-21.5259627525-0.48284089851218.114796329
25.269295719673.04364899972-1.847063876955.9336566757-2.116926233494.119109603330.0379083029542-1.485893919080.02163139963090.330478448867-0.33047267549-0.49662842628-0.3251234841570.3589034824050.1985070080740.3047248906090.0002767448557530.06473510566880.4048065832530.02094677804340.324714096659-10.48230781663.3756112747412.7139449235
32.97135701504-1.573185448590.09111793013236.03123641347-3.31609414313.25589164603-0.160097601395-0.392997000690.003966543885350.4093984533260.0197748990327-0.206941228201-0.2495651698580.5095117305860.1336068246320.216768783272-0.06850498252240.02577143634180.221344080687-0.04812312071880.246389464979-2.475808103058.314223166664.2021388631
46.717107842390.4933238335380.3919135167141.78584382533-0.1912162199123.88502579649-0.07452816341850.2865424654510.421074579816-0.03066711279030.0618975710720.107907549693-0.429383364607-0.257018012748-0.00416446586140.235528538572-0.02570151007120.02773365459840.129082314052-0.009238304777690.153976337325-15.86595183413.0035636886-4.62246710987
51.965636080230.0796327877316-1.531710027221.56101692718-1.972958286123.799855022010.0571256733499-0.09974287764270.240809323820.06751390029670.1409274423310.16680537712-0.359667928428-0.349922994491-0.1379014594140.160074330983-0.006971462507320.03040593233390.277917076706-0.06577600879910.209168037107-26.46300365957.159663169266.88725268105
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 15 )1 - 151 - 15
22chain 'A' and (resid 16 through 48 )16 - 4816 - 48
33chain 'A' and (resid 49 through 83 )49 - 8349 - 83
44chain 'A' and (resid 84 through 129 )84 - 12984 - 128
55chain 'A' and (resid 130 through 184 )130 - 184129 - 183

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