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- PDB-8r8n: Hallucinated de novo TIM barrel with two helical extensions - Hal... -

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Basic information

Entry
Database: PDB / ID: 8r8n
TitleHallucinated de novo TIM barrel with two helical extensions - HalluTIM2-2
ComponentsHalluTIM2-2
KeywordsDE NOVO PROTEIN / Hallucination / TIM barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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: HalluTIM2-2
B: HalluTIM2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5705
Polymers58,2822
Non-polymers2883
Water1448
1
A: HalluTIM2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4294
Polymers29,1411
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HalluTIM2-2


Theoretical massNumber of molelcules
Total (without water)29,1411
Polymers29,1411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.710, 71.200, 88.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 52 or resid 54 through 120 or resid 122 through 242))
d_2ens_1(chain "B" and (resid 3 through 52 or resid 54...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPALAALAAA3 - 524 - 53
d_12ALAALAVALVALAA54 - 12055 - 121
d_13ALAALATHRTHRAA122 - 242123 - 243
d_21ASPASPALAALABB3 - 524 - 53
d_22ALAALAVALVALBB54 - 12055 - 121
d_23ALAALAARGARGBB122 - 176123 - 177
d_24ALAALATHRTHRBB188 - 242189 - 243

NCS oper: (Code: givenMatrix: (-0.582845791642, 0.461710720353, -0.668665831246), (-0.546345625254, 0.386458136078, 0.743072383301), (0.601495836171, 0.798419263151, 0.0270081339391)Vector: 19. ...NCS oper: (Code: given
Matrix: (-0.582845791642, 0.461710720353, -0.668665831246), (-0.546345625254, 0.386458136078, 0.743072383301), (0.601495836171, 0.798419263151, 0.0270081339391)
Vector: 19.7595826098, 31.0568787416, -3.16724085766)

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Components

#1: Protein HalluTIM2-2


Mass: 29140.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium sulfate, 0.1M Tris pH8.6, 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.55→47.63 Å / Num. obs: 19244 / % possible obs: 97.11 % / Redundancy: 4.2 % / Biso Wilson estimate: 91.96 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07381 / Rpim(I) all: 0.04118 / Rrim(I) all: 0.08514 / Net I/σ(I): 8.98
Reflection shellResolution: 2.55→2.641 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.654 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1921 / CC1/2: 0.302 / CC star: 0.681 / Rpim(I) all: 0.8896 / Rrim(I) all: 1.89 / % possible all: 96.36

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Processing

Software
NameVersionClassification
XDS20230630data reduction
PHENIX1.20.1_4487refinement
Coot0.9.8.92model building
PHASER2.8.3phasing
XDS20230630data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→47.63 Å / SU ML: 0.5839 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.8115
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.306 958 5 %
Rwork0.2465 18219 -
obs0.2495 19177 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.94 Å2
Refinement stepCycle: LAST / Resolution: 2.55→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 15 8 3787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263848
X-RAY DIFFRACTIONf_angle_d0.49925178
X-RAY DIFFRACTIONf_chiral_restr0.0427539
X-RAY DIFFRACTIONf_plane_restr0.0033668
X-RAY DIFFRACTIONf_dihedral_angle_d13.95241475
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.65486584776 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.680.4061330.37942552X-RAY DIFFRACTION97.11
2.68-2.850.53241380.44452618X-RAY DIFFRACTION98.89
2.85-3.070.4031370.35622599X-RAY DIFFRACTION98.63
3.07-3.380.31421360.27462587X-RAY DIFFRACTION97.91
3.38-3.870.27951350.23582567X-RAY DIFFRACTION96.16
3.87-4.880.27171380.22332622X-RAY DIFFRACTION96.88
4.88-47.630.2981410.22212674X-RAY DIFFRACTION94.53
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)
14.33886985084-0.645333857807-2.324993897722.074772058230.5128968990083.61275083501-0.04109956103620.2436761586740.0702457169468-0.496721636146-0.0774303667007-0.0142096651526-0.254558080931-0.2388414248730.001245144911110.7035089429710.0507896018828-0.06576579735960.7027543299110.007059573865570.5947647995681.68048697613-34.7243716317-20.473020474
20.977677007151-0.0912415877947-0.3665077834446.65543053182-0.8348675773831.54321086079-0.02450844324380.0349888794341-0.4981024045210.626896926585-0.0667328161399-0.3301211626510.4563479761580.0856440405662-0.0001203377577121.0255250083-0.04550374012170.0434519039710.856362891576-0.06067471748371.1266116506116.48413831641.58723652777-30.3271985317
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 242)AA1 - 2421 - 231
22(chain 'B' and resid 3 through 242)BB3 - 2421 - 230

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