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- PDB-7bif: Crystal structure of v22WRAP-T, a 7-bladed designer protein -

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Basic information

Entry
Database: PDB / ID: 7bif
TitleCrystal structure of v22WRAP-T, a 7-bladed designer protein
Componentsv22WRAP-T
KeywordsDE NOVO PROTEIN / Synthetic Construct
Function / homology
Function and homology information


protein polyubiquitination / metal ion binding / membrane
Similarity search - Function
Borrelia P83100 / : / Borrelia P83/100 protein / AAA-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. ...Borrelia P83100 / : / Borrelia P83/100 protein / AAA-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / 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. / 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: 1.4 Å
AuthorsLee, X.Y. / Mylemans, B. / Laier, I. / 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

Downloads & links

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Assembly

Deposited unit
A: v22WRAP-T
B: v22WRAP-T
C: v22WRAP-T
D: v22WRAP-T


Theoretical massNumber of molelcules
Total (without water)120,2884
Polymers120,2884
Non-polymers00
Water24,4461357
1
A: v22WRAP-T


Theoretical massNumber of molelcules
Total (without water)30,0721
Polymers30,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: v22WRAP-T


Theoretical massNumber of molelcules
Total (without water)30,0721
Polymers30,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: v22WRAP-T


Theoretical massNumber of molelcules
Total (without water)30,0721
Polymers30,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: v22WRAP-T


Theoretical massNumber of molelcules
Total (without water)30,0721
Polymers30,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.853, 72.886, 93.545
Angle α, β, γ (deg.)90.000, 96.002, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
v22WRAP-T


Mass: 30071.877 Da / Num. of mol.: 4 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2J0I0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1357 / 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: 2.29 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium thiocyanate pH 6.9, 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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→57.37 Å / Num. obs: 166377 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 8.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.016 / Rrim(I) all: 0.042 / Net I/σ(I): 25.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 7202 / CC1/2: 0.969 / Rpim(I) all: 0.094 / Rrim(I) all: 0.214 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALS3.0.4data reduction
AimlessCCP4Interface 6.5.000data scaling
PHASERCCP4Interface 6.5.000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ymu

2ymu


Resolution: 1.4→50.07 Å / SU ML: 0.1258 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 17.4355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1813 8273 4.97 %
Rwork0.156 158032 -
obs0.1572 166305 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.3 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8332 0 0 1357 9689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618626
X-RAY DIFFRACTIONf_angle_d1.009611805
X-RAY DIFFRACTIONf_chiral_restr0.10131434
X-RAY DIFFRACTIONf_plane_restr0.00621524
X-RAY DIFFRACTIONf_dihedral_angle_d16.11971217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.21832220.18344506X-RAY DIFFRACTION84.49
1.42-1.430.21842680.17674912X-RAY DIFFRACTION93.86
1.43-1.450.2192990.17625311X-RAY DIFFRACTION99.95
1.45-1.470.20852680.16885253X-RAY DIFFRACTION99.96
1.47-1.490.19652650.16575289X-RAY DIFFRACTION99.84
1.49-1.510.21492770.17645285X-RAY DIFFRACTION99.96
1.51-1.530.21312760.17465295X-RAY DIFFRACTION99.98
1.53-1.550.20433090.16455255X-RAY DIFFRACTION99.93
1.55-1.580.18132740.16015264X-RAY DIFFRACTION99.91
1.58-1.60.20242870.16125320X-RAY DIFFRACTION99.95
1.6-1.630.2162770.16625264X-RAY DIFFRACTION99.95
1.63-1.660.19122820.17015289X-RAY DIFFRACTION99.95
1.66-1.690.20252730.175325X-RAY DIFFRACTION100
1.69-1.730.21162690.16965297X-RAY DIFFRACTION99.91
1.73-1.760.19092700.16875276X-RAY DIFFRACTION99.91
1.76-1.80.19142790.16275305X-RAY DIFFRACTION99.93
1.8-1.850.17443090.15515257X-RAY DIFFRACTION99.96
1.85-1.90.18592870.15485278X-RAY DIFFRACTION99.91
1.9-1.960.17462690.14735304X-RAY DIFFRACTION99.98
1.96-2.020.16342690.15115332X-RAY DIFFRACTION100
2.02-2.090.17592550.15195318X-RAY DIFFRACTION99.96
2.09-2.180.182570.1485304X-RAY DIFFRACTION100
2.18-2.270.17782810.15535351X-RAY DIFFRACTION100
2.27-2.390.20922750.16595283X-RAY DIFFRACTION99.96
2.39-2.540.1833190.15835311X-RAY DIFFRACTION99.89
2.54-2.740.18722510.15775342X-RAY DIFFRACTION100
2.74-3.020.17442690.15655366X-RAY DIFFRACTION100
3.02-3.450.15862710.13935352X-RAY DIFFRACTION100
3.45-4.350.1532940.13465356X-RAY DIFFRACTION100
4.35-50.070.1692720.16085432X-RAY DIFFRACTION99.15

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