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

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Basic information

Entry
Database: PDB / ID: 7udo
TitleCrystal structure of designed helical repeat protein RPB_LRP2_R4 (proteolysis fragment?), forming pseudopolymeric filaments
ComponentsDesigned helical repeat protein (DHR) RPB_LRP2_R4
KeywordsDE NOVO PROTEIN / peptide binding / designed helical repeat (DHR)
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRedler, R.L. / Chang, Y. / 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

Downloads & links

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Assembly

Deposited unit
A: Designed helical repeat protein (DHR) RPB_LRP2_R4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8556
Polymers19,5121
Non-polymers3435
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: See manuscript
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint7 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.620, 72.620, 127.280
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN
Sequence detailsSequence and model reflect a fragment of the larger full-length protein. See methods in referenced ...Sequence and model reflect a fragment of the larger full-length protein. See methods in referenced publication for details.

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium phosphate dibasic, 20% w/v PEG3350

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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: Nov 6, 2019
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: 2.5→44.73 Å / Num. obs: 13974 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 74.18 Å2 / CC1/2: 1 / Rrim(I) all: 0.07 / Net I/σ(I): 18.6
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1002 / CC1/2: 0.48 / Rrim(I) all: 2.18 / % 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: 2.5→44.73 Å / SU ML: 0.4103 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.0718
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 659 5.04 %RANDOM
Rwork0.1925 12425 --
obs0.1938 13084 93.63 %-
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 21 0 1393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121430
X-RAY DIFFRACTIONf_angle_d1.35351915
X-RAY DIFFRACTIONf_chiral_restr0.0691216
X-RAY DIFFRACTIONf_plane_restr0.0068256
X-RAY DIFFRACTIONf_dihedral_angle_d14.3987195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.35721150.34962094X-RAY DIFFRACTION81.06
2.69-2.960.38751270.31722357X-RAY DIFFRACTION90.26
2.96-3.390.26491300.25542548X-RAY DIFFRACTION96.85
3.39-4.270.22371400.20522662X-RAY DIFFRACTION99.57
4.28-44.730.17731470.1442764X-RAY DIFFRACTION99.76
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)
110.0063378513-1.50356467499-1.288820298375.460496951661.482448521097.95828116601-0.15672730650.172003729309-0.2882862306510.2214733092340.120426919440.4433894288210.2184514651530.1335061171940.1092975009870.7437603825740.196762933357-0.0006268843163960.512175268822-0.01862075282160.73062711877733.81177570656.39080377611-25.9788616526
29.51216718397-1.02966453502-3.819281880429.571759742280.1809302186357.32972735965-0.1412978460520.360495259107-0.56619765557-0.4245327668850.135087470510.1480030781940.3232684478120.06341893942520.04646019704110.6643976908870.110394053461-0.001025102560290.467097175382-0.08320469230020.56665282762435.54732934940.653184671134-30.9165636242
37.2244360647-0.832811015690.4514004044299.643988389261.911010643244.450722093310.215609883826-0.159871405354-0.760274744160.1447494630110.08547175927351.125502290420.377396963689-0.514876811516-0.2087457728940.845892627463-0.00327026302349-0.1776946381910.5869760976870.04017535047230.91800405522728.8901609559-9.22388990297-29.8340643948
46.36877029067-0.1967638870330.4533514207977.22735642264-2.885106976958.35105709563-0.134125259177-0.0313781028115-0.429049446490.2960868378480.4643456271170.07614421348180.4279445903350.828945689096-0.1036837191130.9056018362050.276624112725-0.01412638953770.558879519573-0.005873162591190.76719739156838.7974501402-11.9000686057-24.9784265637
57.14020556003-0.383485946471-0.6229279094998.70603257324-1.08368282297.39332918165-0.0590371017736-0.824466945532-0.7395659255380.525463128679-0.3635244390431.075294352590.415551139886-0.921880458691-0.4521018927390.8737524835040.0346011712983-0.004758925159320.8172411872320.1116177918811.0480671781230.8456184082-18.0611511335-18.4959157607
68.55137271454-3.764499207513.24131072235.43375506518-2.187474235017.83309696772-0.1111911578390.234321025777-0.322888065633-0.7823631758890.336855567879-0.2321126447430.1552725749410.1870610878780.1605077437290.8096683650610.122008735475-0.008726046343190.5878676686560.009402132772380.70040403173941.3647913687-21.0137712084-22.2509475146
79.479548292070.7259295097054.534593740638.4444963462.390329138883.61300294586-0.150149299717-1.378688544670.1939474331080.75550946136-0.2748911362610.6488374351530.0190990437618-0.6653415986930.1520726499660.836843152094-0.03037642666590.0401005142370.8568369346280.1672487809750.80021284838240.5708629473-23.1994846365-10.9191418404
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 22 )0 - 221 - 24
22chain 'A' and (resid 23 through 62 )23 - 6225 - 64
33chain 'A' and (resid 63 through 83 )63 - 8365 - 86
44chain 'A' and (resid 84 through 105 )84 - 10587 - 109
55chain 'A' and (resid 106 through 125 )106 - 125110 - 129
66chain 'A' and (resid 126 through 147 )126 - 147130 - 152
77chain 'A' and (resid 148 through 171 )148 - 171153 - 176

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