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- PDB-5bvl: Crystal structure of a de novo designed TIM-barrel -

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Basic information

Entry
Database: PDB / ID: 5bvl
TitleCrystal structure of a de novo designed TIM-barrel
Componentsdesigned TIM barrel sTIM11
KeywordsDE NOVO PROTEIN / TIM-barrel / computational design / idealized scaffold
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.992 Å
AuthorsFeldmeier, K. / Hocker, B.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.
Authors: Huang, P.S. / Feldmeier, K. / Parmeggiani, F. / Fernandez Velasco, D.A. / Hocker, B. / Baker, D.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Dec 30, 2015Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: designed TIM barrel sTIM11


Theoretical massNumber of molelcules
Total (without water)22,8961
Polymers22,8961
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.080, 50.080, 131.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein designed TIM barrel sTIM11


Mass: 22896.449 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)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.8 Å3/Da / Density % sol: 31.7 % / Description: Needle
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG 3350, 0.2M magnesium chloride hexahydrate, 0.1M bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2014
RadiationMonochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.992→46.79 Å / Num. obs: 11894 / % possible obs: 98.26 % / Redundancy: 5.86 % / Biso Wilson estimate: 41.84 Å2 / Rmerge(I) obs: 0.05804 / Net I/σ(I): 15.24
Reflection shellResolution: 1.992→2.064 Å / Rmerge(I) obs: 0.6607 / Mean I/σ(I) obs: 1.79 / % possible all: 93.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosetta backbone model

Resolution: 1.992→46.79 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2607 595 5 %
Rwork0.2237 --
obs0.2254 11894 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.9 Å2
Refinement stepCycle: LAST / Resolution: 1.992→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 0 20 1481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131486
X-RAY DIFFRACTIONf_angle_d1.2152010
X-RAY DIFFRACTIONf_dihedral_angle_d16.025541
X-RAY DIFFRACTIONf_chiral_restr0.05211
X-RAY DIFFRACTIONf_plane_restr0.006260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9923-2.19280.26351420.24382707X-RAY DIFFRACTION97
2.1928-2.51010.2911480.2432797X-RAY DIFFRACTION100
2.5101-3.16240.28611490.26552836X-RAY DIFFRACTION100
3.1624-46.80390.24541560.20352959X-RAY DIFFRACTION97

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