[English] 日本語
Yorodumi
- PDB-7udo: Crystal structure of designed helical repeat protein RPB_LRP2_R4 ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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


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


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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more