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- PDB-7ue2: Crystal structure of designed helical repeat protein RPB_PLP3_R6 ... -

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Basic information

Entry
Database: PDB / ID: 7ue2
TitleCrystal structure of designed helical repeat protein RPB_PLP3_R6 bound to PLPx6 peptide
Components
  • PLPx6 peptide
  • RPB_PLP3_R6
KeywordsDE NOVO PROTEIN / peptide binding
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsChang, Y. / Ekiert, D.C. / Bhabha, G.
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 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 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

Downloads & links

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Assembly

Deposited unit
A: RPB_PLP3_R6
B: PLPx6 peptide


Theoretical massNumber of molelcules
Total (without water)35,7562
Polymers35,7562
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-27 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.470, 124.470, 104.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein RPB_PLP3_R6


Mass: 33796.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide PLPx6 peptide


Mass: 1959.454 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.4 M ammonium sulfate, 0.1 M trisodium citrate, pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 31, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.68→45.1 Å / Num. obs: 11891 / % possible obs: 92.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 69.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1129 / Rpim(I) all: 0.03229 / Rrim(I) all: 0.1175 / Rsym value: 0.1129 / Net I/σ(I): 18.5
Reflection shellResolution: 2.68→2.78 Å / Redundancy: 1.21 % / Num. unique obs: 1169 / CC1/2: 0.514 / % possible all: 77.42

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational Design Model

Resolution: 2.68→45.08 Å / SU ML: 0.425 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.9879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2771 547 4.99 %
Rwork0.2259 10412 -
obs0.2283 10959 92.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.93 Å2
Refinement stepCycle: LAST / Resolution: 2.68→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 0 0 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232546
X-RAY DIFFRACTIONf_angle_d0.47443433
X-RAY DIFFRACTIONf_chiral_restr0.0305402
X-RAY DIFFRACTIONf_plane_restr0.0029435
X-RAY DIFFRACTIONf_dihedral_angle_d4.1397334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.950.46141140.36992242X-RAY DIFFRACTION81.05
2.95-3.380.32871350.30132500X-RAY DIFFRACTION90.02
3.38-4.250.26781430.23962748X-RAY DIFFRACTION97.83
4.25-45.080.2441550.18272922X-RAY DIFFRACTION99.16
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)
10.191919666877-0.1628746868420.03342774472280.507961155864-0.3262710355530.8196328051420.144592312020.250583286301-0.5806942960720.0518365812452-0.3006623918140.09165738194840.1077875923450.235998364309-4.09315597621E-50.6903050542960.0919518375382-0.03149008774870.5983304994480.0192971113080.915375323657-33.7313159985-22.1190016894-44.1691905454
21.16878324532-0.2562234586751.30015829222.472354203180.1098794118921.533524018950.1486699356960.1684620656060.151210580382-0.03061077986280.006391328098730.471101593198-0.075737687448-0.179264217962-8.85391181892E-50.5872078770.02101015106570.07268936250240.5571873563380.05005509988570.628121194612-37.1479383707-2.60179743189-36.3046907901
30.947699620980.748270554730.01823829163082.241131744930.4003697607032.13061194352-0.0173253377565-0.4781654097490.1893239565980.3590739732370.0129923186252-0.337806396266-0.05793955878670.00217031206218-2.46013244644E-50.6261556498080.013003957260.03310382922270.64329034706-0.01342837989920.576792603655-22.846541212815.3828026513-23.8805651197
40.0466886511482-0.0141456014420.03014229029560.02927522437520.002542898891750.02571317348310.671963833159-0.0914413530671-0.3541304801630.0151078915120.0226372145454-0.0543898242547-0.215862360173-0.192117026370.001080075378180.622194348720.158778156311-0.2719498748490.708258778518-0.04561793007390.873958265723-32.1158298201-22.8476433363-33.6810429624
50.105675678292-0.04994059267030.02870795750630.0349768350896-0.02071059116990.0112084740121-0.009638801712910.314304430393-0.0829683825616-0.7522633534560.0587014366259-0.006188917424240.2067682846470.0296830078749-0.0001483001667930.7239950790920.0475020145890.1656315175970.5297842858310.007143709394790.69587184556-26.5582737248-2.86299729064-32.6045506602
60.03549956452850.00050924021542-0.01725407570070.0769684168052-0.03436185873990.0230281511530.07218538647220.749400765020.3546302708860.220880308379-0.136229582634-0.185339662410.2677933384050.01739362099270.0008711012202260.5205575104950.1088883831620.05058778342840.7127251184920.09294751402360.372827235752-20.809340975116.7296357467-35.8780642076
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 51 )AA0 - 511 - 52
22chain 'A' and (resid 52 through 201 )AA52 - 20153 - 202
33chain 'A' and (resid 202 through 303 )AA202 - 303203 - 304
44chain 'B' and (resid -9 through -5 )BB-9 - -51 - 5
55chain 'B' and (resid -4 through 5 )BB-4 - 56 - 15
66chain 'B' and (resid 6 through 9 )BB6 - 916 - 19

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