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- PDB-7bid: Crystal structure of v31WRAP-T, a 7-bladed designer protein -

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Basic information

Entry
Database: PDB / ID: 7bid
TitleCrystal structure of v31WRAP-T, a 7-bladed designer protein
Componentsv31WRAP-T
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology
Function and homology information


microtubule organizing center organization / microtubule plus-end binding / retrograde axonal transport / microtubule associated complex / dynein complex binding / cytoplasmic microtubule / kinetochore / neuron projection / neuronal cell body / membrane / metal ion binding
Similarity search - Function
Borrelia P83100 / Borrelia P83/100 protein / AAA-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...Borrelia P83100 / Borrelia P83/100 protein / AAA-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
WD-40 repeat protein
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLaier, I. / Mylemans, B. / Lee, X.Y. / Voet, A.R.D.
Funding support Belgium, 4items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0E4717N Belgium
Research Foundation - Flanders (FWO)G0F9316N Belgium
Research Foundation - Flanders (FWO)G051917N Belgium
Research Foundation - Flanders (FWO)GBM-D3229-ASP/17 Belgium
CitationJournal: Sci Rep / Year: 2021
Title: Structure and stability of the designer protein WRAP-T and its permutants.
Authors: Mylemans, B. / Lee, X.Y. / Laier, I. / Helsen, C. / Voet, A.R.D.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: v31WRAP-T


Theoretical massNumber of molelcules
Total (without water)30,3541
Polymers30,3541
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.636, 61.396, 99.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein v31WRAP-T


Mass: 30354.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: GSHMQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVTGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVTGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVTGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVTGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVTGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVTGVAFSPDGQTIASASDDKTVKLWNRNGQLLQTLTGHSSSVTGVAFSPDG
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: B2J0I0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium formate 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→44.64 Å / Num. obs: 26008 / % possible obs: 99.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 11.32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.01 / Χ2: 0.89 / Net I/σ(I): 55.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5 % / Rmerge(I) obs: 0.042 / Mean I/σ(I) obs: 21.6 / Num. unique obs: 7304 / CC1/2: 0.998 / Rpim(I) all: 0.019 / Χ2: 0.5 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ymu

2ymu


Resolution: 1.8→40.72 Å / SU ML: 0.1424 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 16.9653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1827 1318 5.08 %
Rwork0.1476 24635 -
obs0.1494 25953 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.81 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 0 326 2395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01582200
X-RAY DIFFRACTIONf_angle_d1.33933022
X-RAY DIFFRACTIONf_chiral_restr0.1014364
X-RAY DIFFRACTIONf_plane_restr0.0089397
X-RAY DIFFRACTIONf_dihedral_angle_d15.6911761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.22071570.1512612X-RAY DIFFRACTION97.81
1.87-1.960.24881490.1542682X-RAY DIFFRACTION99.86
1.96-2.060.18441510.14512696X-RAY DIFFRACTION99.89
2.06-2.190.19511450.1472720X-RAY DIFFRACTION100
2.19-2.360.19651500.14782727X-RAY DIFFRACTION100
2.36-2.60.2011410.15412727X-RAY DIFFRACTION100
2.6-2.970.21841230.15912772X-RAY DIFFRACTION100
2.97-3.740.13911510.13912779X-RAY DIFFRACTION100
3.74-40.720.15311510.14332920X-RAY DIFFRACTION99.74

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