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- PDB-8r8o: Hallucinated de novo TIM barrel with three helical extensions - H... -

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Basic information

Entry
Database: PDB / ID: 8r8o
TitleHallucinated de novo TIM barrel with three helical extensions - HalluTIM3-1
ComponentsHalluTIM3-1
KeywordsDE NOVO PROTEIN / Hallucination / TIM barrel
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBeck, J. / Shanmugaratnam, S. / Hocker, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: Diversifying de novo TIM barrels by hallucination.
Authors: Beck, J. / Shanmugaratnam, S. / Hocker, B.
History
DepositionNov 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HalluTIM3-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,87514
Polymers32,0251
Non-polymers85013
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-73 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.360, 122.360, 165.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HalluTIM3-1


Mass: 32024.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 63 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% Glycerol, 1.55M Ammoniumsulfate, 0.08M Sodium acetate pH 4.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2023
RadiationMonochromator: Oxford-FMB, UK; Si(111) or Si(311); both crystals LN2 cooled, fixed exit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→38.23 Å / Num. obs: 40404 / % possible obs: 99.54 % / Redundancy: 39.3 % / Biso Wilson estimate: 67.89 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1358 / Rpim(I) all: 0.02208 / Rrim(I) all: 0.1376 / Net I/σ(I): 17.65
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 41.6 % / Rmerge(I) obs: 5.774 / Mean I/σ(I) obs: 0.46 / Num. unique obs: 3948 / CC1/2: 0.342 / CC star: 0.714 / Rpim(I) all: 0.8997 / Rrim(I) all: 5.845 / % possible all: 95.95

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20230630data reduction
Coot0.9.8.92model building
PHASER2.8.3phasing
XDS20230630data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→38.23 Å / SU ML: 0.3974 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.0344
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2598 2008 4.99 %
Rwork0.2453 38227 -
obs0.246 40235 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.96 Å2
Refinement stepCycle: LAST / Resolution: 2.15→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 47 50 2237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172263
X-RAY DIFFRACTIONf_angle_d0.41853046
X-RAY DIFFRACTIONf_chiral_restr0.0383308
X-RAY DIFFRACTIONf_plane_restr0.0036407
X-RAY DIFFRACTIONf_dihedral_angle_d3.9602323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.48621310.50332534X-RAY DIFFRACTION94.54
2.2-2.260.4431400.3872690X-RAY DIFFRACTION99.82
2.26-2.330.3861410.34672673X-RAY DIFFRACTION99.96
2.33-2.410.35291420.31552698X-RAY DIFFRACTION99.96
2.41-2.490.31631420.2982711X-RAY DIFFRACTION100
2.49-2.590.30451420.29682685X-RAY DIFFRACTION99.96
2.59-2.710.36991430.32562717X-RAY DIFFRACTION99.97
2.71-2.850.35971430.29852718X-RAY DIFFRACTION100
2.85-3.030.25871430.27992731X-RAY DIFFRACTION100
3.03-3.260.30941440.26522725X-RAY DIFFRACTION100
3.26-3.590.2641450.24112759X-RAY DIFFRACTION100
3.59-4.110.21241460.21352778X-RAY DIFFRACTION100
4.11-5.180.20591490.20242823X-RAY DIFFRACTION99.97
5.18-38.230.25791570.23972985X-RAY DIFFRACTION99.78
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)
10.5850148832650.725867069267-0.1993538386611.24962560365-0.5990456704950.4205912306560.345747419825-0.3434585766870.2249018188450.721733248913-0.06048002096020.9090784226210.0853596776409-0.728693365135-0.005111217488381.20116656223-0.40491369825-0.00779410037771.080498615910.01892816770140.887252396964-57.82999111948.7353064841633.2675620243
21.129812428860.4514705310280.5604413399432.254263845451.248085514263.249339769990.177645800840.0400755722488-0.03530296806020.0750628216685-0.0927187709739-0.372665553887-0.0811051459050.316566242758-0.0004555727967570.636106150299-0.127306050558-0.05560387646390.447226162391-0.0003493143256330.611832159242-43.57077199839.2819028011410.7662564609
30.622996040234-0.8673357920.04340174417211.446924705930.3737549538920.7896634414870.701956939814-0.35774603503-0.5980432395971.18392594351-0.0441573677792-0.8768045926780.9961946422110.760413870007-0.0004557693120751.11836622011-0.106812300613-0.3174596650251.00776578335-0.08201405834450.952359658883-35.86668459038.2464167755629.8902293628
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 41 through 89 )41 - 8935 - 83
22chain 'A' and (resid 90 through 268 )90 - 26884 - 262
33chain 'A' and (resid 7 through 40 )7 - 401 - 34

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