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- PDB-7udl: Crystal structure of designed helical repeat protein RPB_PLP1_R6 ... -

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Basic information

Entry
Database: PDB / ID: 7udl
TitleCrystal structure of designed helical repeat protein RPB_PLP1_R6 bound to PLPx6 peptide
Components
  • 6xPLP Peptide
  • Designed helical repeat protein (DHR) RPB_PLP1_R6
KeywordsDE NOVO PROTEIN / peptide binding / designed helical repeat (DHR)
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed helical repeat protein (DHR) RPB_PLP1_R6
B: 6xPLP Peptide
D: 6xPLP Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3294
Polymers36,2673
Non-polymers621
Water1267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: See manuscript
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.440, 99.440, 173.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Designed helical repeat protein (DHR) RPB_PLP1_R6


Mass: 31927.193 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 6xPLP Peptide


Mass: 2169.727 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 40% v/v MPD, 0.1 M sodium phosphate-citrate, pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2021
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→37.7 Å / Num. obs: 18220 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 59.77 Å2 / CC1/2: 1 / Rrim(I) all: 0.06 / Net I/σ(I): 18.1
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1327 / CC1/2: 0.45 / Rrim(I) all: 2.45 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model

Resolution: 2.15→37.68 Å / SU ML: 0.3393 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 1672 9.88 %RANDOM
Rwork0.2323 15249 --
obs0.2366 16921 92.85 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.91 Å2
Refinement stepCycle: LAST / Resolution: 2.15→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 4 7 2374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00162450
X-RAY DIFFRACTIONf_angle_d0.41223342
X-RAY DIFFRACTIONf_chiral_restr0.0284411
X-RAY DIFFRACTIONf_plane_restr0.0023441
X-RAY DIFFRACTIONf_dihedral_angle_d11.0646945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.45271160.3979981X-RAY DIFFRACTION72.99
2.21-2.280.35241060.32981078X-RAY DIFFRACTION80.05
2.28-2.370.34431230.29821168X-RAY DIFFRACTION86.3
2.37-2.460.31631340.29451241X-RAY DIFFRACTION90.7
2.46-2.570.33591360.2811264X-RAY DIFFRACTION94.02
2.57-2.710.30611430.29911289X-RAY DIFFRACTION94.77
2.71-2.880.31851440.26981317X-RAY DIFFRACTION97.4
2.88-3.10.36911510.291347X-RAY DIFFRACTION98.49
3.1-3.410.34341520.26111361X-RAY DIFFRACTION99.08
3.41-3.910.26941520.22491371X-RAY DIFFRACTION99.8
3.91-4.920.22391540.19631384X-RAY DIFFRACTION99.94
4.92-37.680.24481610.20541448X-RAY DIFFRACTION99.75
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)
16.74317862578-1.621616741832.630022356257.0289711964-3.205196579927.18645526859-0.07333380500790.4138724728190.08362369507570.07755137266150.03200237459160.308719046617-0.710967258418-0.817250791096-0.05511848298650.424324707653-0.004244033184610.07285882379830.812412641790.04329950953880.4225982821791.82047754249-32.8457914181-4.63458020571
27.83549174574-2.437015673486.377435276946.070787627820.546435728119.11144603577-0.0453225236221-0.607609593162-1.152758876750.4753779134790.5253546872940.812477339544-0.10336901443-0.800582839468-0.2296362165010.4953468633870.02087466478170.09942818453780.503849223680.2240228038540.71378972311112.6808851676-45.303749246312.5911007913
38.46663240114-2.834635107821.691901724718.950429089023.361061325557.70350593003-0.209698482969-0.495327338205-0.2312997952970.574149520560.4162563579710.133782260759-0.4608777909680.0679199008213-0.2934897252840.5898315049180.112719570828-0.005815332740480.5477315221120.03512530261480.4807522951328.1150567654-43.218505617326.4232612642
42.162103146181.597322681350.4228683316484.420611408223.168724590322.597102942730.5537263022612.761510590321.21300332336-3.14906516992-1.405087342750.0480934872071-1.82858540494-0.301549679384-0.1846394287141.108193208820.1308952502690.05449899102031.357111691460.45697904740.63292249346812.1676010918-27.0248647464-18.3553230962
57.22792517775-1.042945841524.674909490952.394274456620.234823211653.36356904059-0.8449196941640.7207900685640.5108161935530.4006095178190.2314325345460.00017376188778-0.7631206585170.7191595176390.4730049270460.7276780397560.1389188726650.020082023520.333376955190.03894071760360.42227462289615.0739380316-32.83654659987.93238576292
63.412439079012.47003715491-2.228632993192.89661354875-0.05318225801873.58366111136-0.6356323241120.512279639333-0.55116580449-0.5164400144420.6188163089361.135768018340.206107643021-0.674447383130.1709624033141.219983005680.5286036011350.1917223508541.378936777950.1517106322770.65301739754514.7608635325-25.74665611351.18118606206
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 116 )AA3 - 1161 - 114
22chain 'A' and (resid 117 through 211 )AA117 - 211115 - 211
33chain 'A' and (resid 212 through 280 )AA212 - 280212 - 283
44chain 'B' and (resid 3 through 7 )BC3 - 71 - 5
55chain 'B' and (resid 8 through 21 )BC8 - 216 - 19
66chain 'D' and (resid 203 through 216 )DD203 - 2161 - 14

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