[English] 日本語
Yorodumi
- PDB-7udm: Crystal structure of designed helical repeat protein RPB_PLP1_R6 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7udm
TitleCrystal structure of designed helical repeat protein RPB_PLP1_R6 in alternative conformation 1 (with peptide)
Components
  • 6xPLP
  • 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: 2.65 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 / Refinement description
Category: citation / citation_author ...citation / citation_author / refine_ls_restr_ncs / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_oper
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_PLP1_R6
B: Designed helical repeat protein (DHR) RPB_PLP1_R6
C: 6xPLP


Theoretical massNumber of molelcules
Total (without water)65,8593
Polymers65,8593
Non-polymers00
Water00
1
A: Designed helical repeat protein (DHR) RPB_PLP1_R6


Theoretical massNumber of molelcules
Total (without water)31,9981
Polymers31,9981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Designed helical repeat protein (DHR) RPB_PLP1_R6


Theoretical massNumber of molelcules
Total (without water)31,9981
Polymers31,9981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 6xPLP


Theoretical massNumber of molelcules
Total (without water)1,8621
Polymers1,8621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.380, 80.260, 154.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

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


Mass: 31998.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli B (bacteria)
#2: Protein/peptide 6xPLP


Mass: 1862.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.02 M calcium chloride, 30% v/v MPD, 0.1 M sodium acetate, pH 4.6

-
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: Feb 16, 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: 2.65→43.22 Å / Num. obs: 20350 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 69.44 Å2 / CC1/2: 1 / Rrim(I) all: 0.1 / Net I/σ(I): 10.9
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 6.7 % / Num. unique obs: 1492 / CC1/2: 0.57 / Rrim(I) all: 2.11 / % possible all: 100

-
Processing

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

Resolution: 2.65→43.22 Å / SU ML: 0.4361 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 40.3997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 1167 6.45 %RANDOM
Rwork0.2597 16916 --
obs0.2623 18083 88.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.68 Å2
Refinement stepCycle: LAST / Resolution: 2.65→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 0 0 4544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00134615
X-RAY DIFFRACTIONf_angle_d0.2946233
X-RAY DIFFRACTIONf_chiral_restr0.0289748
X-RAY DIFFRACTIONf_plane_restr0.0013823
X-RAY DIFFRACTIONf_dihedral_angle_d21.98521815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.770.45891130.45631719X-RAY DIFFRACTION73.4
2.77-2.920.43221310.35871797X-RAY DIFFRACTION78.12
2.92-3.10.35011310.35781932X-RAY DIFFRACTION81.96
3.1-3.340.35411420.32812078X-RAY DIFFRACTION88.73
3.34-3.670.3731500.28352211X-RAY DIFFRACTION93.39
3.67-4.210.29011620.24112290X-RAY DIFFRACTION96.04
4.21-5.30.26841640.23862377X-RAY DIFFRACTION99.22
5.3-43.220.25861740.22312512X-RAY DIFFRACTION99.19
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)
17.29733301711-2.56494773908-0.5891045690883.59335131575-2.669637762823.14925315686-1.24375367085-0.7915161894710.466593795942-2.036209477150.7028115089453.1000492680.0163254433104-1.594217504370.213633402481.753467118180.00876363817697-0.4051882056021.01274007660.008449430649881.097051188765.2333647874112.795288006520.9401225435
23.842817612393.344362070770.4926748360218.02909050275-0.2278192803690.877531156435-0.0957298941806-0.2213041986530.4194819935261.059357016130.05150772052071.327852444691.14280210398-0.07599030878470.130781207031.59630227035-0.0370173074699-0.002216897384110.4581209070730.07068096928730.5481638671120.296960140726.149502765130.9444037352
33.45423024062.455903427053.152007841933.469513912382.513245258424.47571574046-0.06803898169350.2443489787510.135997899194-0.4743721108740.19094732498-0.05822326742310.1759081512850.0287823095919-0.143416130931.54768754568-0.02821602633170.0998888756690.5076210151490.03464969819980.57806625653226.37025043726.852080902121.9129130212
42.415480317562.129597874634.34462959473.396539158583.420971688759.765992878530.1226143282320.485268590149-0.505905558466-0.2366425589650.477822200933-0.5219924568050.8972123112930.942259205348-0.6169478217641.297969564170.1092113087160.2729219202720.630420836759-0.05688813636740.78825577340737.332112876322.167242296626.646780433
56.02273724164-4.39905712417-4.087995071146.757060807654.521455826286.718131826490.1739589810070.0646364677947-0.00799689980603-0.0826222660556-0.31098839722-0.0228393852429-0.506794647462-0.702534103140.1465783338031.214839628940.0833955125558-0.02213884931470.4603839004440.02729572348590.56028444236224.361407995717.928170680656.4676174957
64.03346965245-1.19767359025-3.070766025292.34105610441.317461210456.804524406950.257715592704-0.0640717317914-0.1396803246430.177097271637-0.140488865003-0.257141847477-0.7789500833390.301421189813-0.09818350883991.409558901660.0365968472501-0.1029410512630.4206561984370.03307409442560.75376008709238.636891308420.773030558457.9592351607
75.928046947180.316741600434-0.8352985226774.96419329555-3.870166980453.637711299620.3784809496251.160722345620.270460820144-1.601070827490.335909015568-0.579515107359-0.0567173280264-0.392702406517-0.03088713888062.322231765560.259454605503-0.03542880165360.7110522755850.07681874725731.0444313051231.540744854715.926587900437.6761459384
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 25 )AA0 - 251 - 26
22chain 'A' and (resid 26 through 70 )AA26 - 7027 - 73
33chain 'A' and (resid 71 through 211 )AA71 - 21174 - 215
44chain 'A' and (resid 212 through 279 )AA212 - 279216 - 283
55chain 'B' and (resid 1 through 117 )BB1 - 1171 - 117
66chain 'B' and (resid 118 through 281 )BB118 - 281118 - 282
77chain 'C' and (resid 1 through 12 )CC1 - 121 - 12

+
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