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- PDB-7udk: Crystal structure of designed helical repeat protein RPB_LRP2_R4 ... -

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Basic information

Entry
Database: PDB / ID: 7udk
TitleCrystal structure of designed helical repeat protein RPB_LRP2_R4 bound to LRPx4 peptide
Components
  • 4xLRP
  • Designed helical repeat protein (DHR) RPB_LRP2_R4
KeywordsDE NOVO PROTEIN / peptide binding / designed helical repeat (DHR)
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsChang, Y. / Redler, R.L. / Bhabha, G. / Ekiert, D.C.
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
A: Designed helical repeat protein (DHR) RPB_LRP2_R4
B: 4xLRP


Theoretical massNumber of molelcules
Total (without water)21,0002
Polymers21,0002
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-9 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.780, 70.780, 128.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Designed helical repeat protein (DHR) RPB_LRP2_R4


Mass: 19512.117 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)
#2: Protein/peptide 4xLRP


Mass: 1487.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 4.41 Å3/Da / Density % sol: 72.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, pH 7, 10% 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-B / Wavelength: 1.0329 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2021
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0329 Å / Relative weight: 1
ReflectionResolution: 3.18→35.39 Å / Num. obs: 6621 / % possible obs: 89.05 % / Redundancy: 9.8 % / Biso Wilson estimate: 132.61 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08023 / Rpim(I) all: 0.02691 / Rrim(I) all: 0.08474 / Rsym value: 0.08023 / Net I/σ(I): 14.13
Reflection shellResolution: 3.18→3.294 Å / Num. unique obs: 633 / CC1/2: 0.687

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model

Resolution: 3.18→35.39 Å / SU ML: 0.2247 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.2479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2555 294 4.98 %
Rwork0.2071 5610 -
obs0.2096 5904 89.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 161.92 Å2
Refinement stepCycle: LAST / Resolution: 3.18→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 0 0 1476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391490
X-RAY DIFFRACTIONf_angle_d0.61621998
X-RAY DIFFRACTIONf_chiral_restr0.042228
X-RAY DIFFRACTIONf_plane_restr0.0057266
X-RAY DIFFRACTIONf_dihedral_angle_d3.786198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-4.010.35151260.33112418X-RAY DIFFRACTION78.93
4.01-35.390.23751680.18453192X-RAY DIFFRACTION98.71
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)
15.641169240060.4476181637350.8945863073327.42831041268-1.351933263695.039080424910.473108986651-0.36613018438-0.1423230247910.0892310862198-0.0857225596909-0.482648742872-0.2383036133520.156991597996-0.392868026051.655322582070.398531387781-0.01343816777861.073462997550.0708168456831.08334336499-32.90052511330.852334381691-30.0351110653
25.579990555051.213354125090.2762103837752.7664753143-3.089992264956.6388284953-0.8452230221430.02670892005890.8274007566170.1251787920620.7841913750060.3866219249090.128678680681-1.55735887421-0.2094539023712.464969179280.8955713067360.2889758470520.843876999727-0.2391199411361.26211486053-37.40475224412.080765743-23.616310807
37.28391287121-3.521338316231.306927145199.485133321923.04893148749.01786036777-0.451441790116-0.791465068966-0.0997821111228-0.1210889180420.591921096228-0.979184335523-0.7484917246720.937258270088-0.1885169247261.260213510860.04038842453340.0655207879471.07015631024-0.1411617908251.12824363625-36.202476826920.9204951281-17.0313464572
43.03882118609-3.099466839930.8096913568063.092832997470.1256327754993.45118893493-2.86995805075-1.199547591022.192168017294.192042169752.0126730693-2.88387373515-0.693250790848-1.467609235560.2264175550631.577244361940.446621492253-0.2871095688541.58877258701-0.2260398334071.75954029374-43.15855814856.3322432881-21.5863536435
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 86 )AA0 - 861 - 87
22chain 'A' and (resid 87 through 105 )AA87 - 10588 - 106
33chain 'A' and (resid 106 through 171 )AA106 - 171107 - 172
44chain 'B' and (resid -2 through 9 )BB-2 - 91 - 12

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