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- PDB-7udj: Crystal structure of designed helical repeat protein RPB_PEW3_R4 ... -

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Basic information

Entry
Database: PDB / ID: 7udj
TitleCrystal structure of designed helical repeat protein RPB_PEW3_R4 bound to PAWx4 peptide
Components
  • 4xPAW peptide
  • De novo designed helical repeat protein RPB_PEW3_R4
KeywordsDE NOVO PROTEIN / Synthetic protein / designed helical repeat protein / peptide binder
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRedler, R.L. / Chang, Y. / Bhabha, G. / Ekiert, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128777 United States
CitationJournal: Nature / Year: 2023
Title: De novo design of modular peptide-binding proteins by superhelical matching.
Authors: Wu, K. / Bai, H. / Chang, Y.T. / Redler, R. / McNally, K.E. / Sheffler, W. / Brunette, T.J. / Hicks, D.R. / Morgan, T.E. / Stevens, T.J. / Broerman, A. / Goreshnik, I. / DeWitt, M. / Chow, C. ...Authors: Wu, K. / Bai, H. / Chang, Y.T. / Redler, R. / McNally, K.E. / Sheffler, W. / Brunette, T.J. / Hicks, D.R. / Morgan, T.E. / Stevens, T.J. / Broerman, A. / Goreshnik, I. / DeWitt, M. / Chow, C.M. / Shen, Y. / Stewart, L. / Derivery, E. / Silva, D.A. / Bhabha, G. / Ekiert, D.C. / Baker, D.
History
DepositionMar 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: 4xPAW peptide
H: De novo designed helical repeat protein RPB_PEW3_R4


Theoretical massNumber of molelcules
Total (without water)22,8092
Polymers22,8092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-15 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 67.600, 71.300
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/peptide 4xPAW peptide


Mass: 1435.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein De novo designed helical repeat protein RPB_PEW3_R4


Mass: 21373.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli B (bacteria)

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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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MES, pH 5, 30% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2019
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.7→38.3 Å / Num. obs: 6383 / % possible obs: 99.62 % / Redundancy: 6.1 % / Biso Wilson estimate: 92.18 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.06972 / Rpim(I) all: 0.03122 / Rrim(I) all: 0.07664 / Net I/σ(I): 12.04
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.056 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 612 / CC1/2: 0.808 / Rpim(I) all: 0.444 / Rrim(I) all: 1.147 / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.16-3549-0000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model

Resolution: 2.7→38.3 Å / SU ML: 0.4486 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.2494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2704 316 4.96 %RANDOM
Rwork0.2454 6057 --
obs0.2467 6373 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.91 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 0 0 1606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00161627
X-RAY DIFFRACTIONf_angle_d0.40642198
X-RAY DIFFRACTIONf_chiral_restr0.0288252
X-RAY DIFFRACTIONf_plane_restr0.0023290
X-RAY DIFFRACTIONf_dihedral_angle_d10.89571004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.40.33051540.32242966X-RAY DIFFRACTION99.7
3.4-38.30.26011620.23073091X-RAY DIFFRACTION99.57
Refinement TLS params.Method: refined / Origin x: -4.69073608352 Å / Origin y: 10.8001177745 Å / Origin z: -15.7001410167 Å
111213212223313233
T0.936999298107 Å20.0526791361269 Å20.107826749706 Å2-0.878876753353 Å2-0.0380459411827 Å2--0.989968430863 Å2
L2.87733854926 °20.989953469839 °20.54483620355 °2-2.41385610431 °20.641048822901 °2--2.28727170323 °2
S-0.0780953222183 Å °0.0535710525337 Å °-0.0480430855582 Å °-0.354288186773 Å °-0.00265694971785 Å °0.0144314022264 Å °-0.27018598087 Å °-0.0705369110623 Å °-0.000157040928673 Å °
Refinement TLS groupSelection details: all

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