[English] 日本語
Yorodumi
- PDB-9dcz: Designed allosteric facilitated dissociation switch AS1 in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dcz
TitleDesigned allosteric facilitated dissociation switch AS1 in complex state TH with methylated lysines, crystal #1
Components
  • Designed allosteric facilitated dissociation switch AS1 H
  • Designed allosteric facilitated dissociation switch AS1 T
KeywordsDE NOVO PROTEIN / design model / Effector / kinetics and dynamics / Protein-protein interactions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBera, A.K. / Broerman, A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Design of facilitated dissociation enables temporal control over cytokine signaling
Authors: Broerman, P. / Bera, A.K. / Baker, D.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Designed allosteric facilitated dissociation switch AS1 H
B: Designed allosteric facilitated dissociation switch AS1 T
C: Designed allosteric facilitated dissociation switch AS1 H
D: Designed allosteric facilitated dissociation switch AS1 T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2235
Polymers88,1054
Non-polymers1181
Water1267
1
A: Designed allosteric facilitated dissociation switch AS1 H
B: Designed allosteric facilitated dissociation switch AS1 T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1713
Polymers44,0522
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-13 kcal/mol
Surface area18130 Å2
MethodPISA
2
C: Designed allosteric facilitated dissociation switch AS1 H
D: Designed allosteric facilitated dissociation switch AS1 T


Theoretical massNumber of molelcules
Total (without water)44,0522
Polymers44,0522
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-4 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.710, 80.710, 546.856
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein Designed allosteric facilitated dissociation switch AS1 H


Mass: 29283.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Designed allosteric facilitated dissociation switch AS1 T


Mass: 14768.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Sodium malonate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2024
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.9→34.75 Å / Num. obs: 44094 / % possible obs: 99.9 % / Redundancy: 31.4 % / Biso Wilson estimate: 66.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.369 / Rpim(I) all: 0.067 / Net I/σ(I): 10.5
Reflection shellResolution: 2.9→2.94 Å / Redundancy: 34.2 % / Rmerge(I) obs: 2.128 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3898 / CC1/2: 0.876 / Rpim(I) all: 0.369 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→34.75 Å / SU ML: 0.4261 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.0221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.255 3534 8.01 %
Rwork0.2094 40560 -
obs0.213 44094 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6010 0 8 7 6025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256051
X-RAY DIFFRACTIONf_angle_d0.50868141
X-RAY DIFFRACTIONf_chiral_restr0.0362967
X-RAY DIFFRACTIONf_plane_restr0.00461029
X-RAY DIFFRACTIONf_dihedral_angle_d21.34592330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.4581440.37791626X-RAY DIFFRACTION99.89
2.94-2.980.37111490.32661652X-RAY DIFFRACTION99.78
2.98-3.030.41891400.32751581X-RAY DIFFRACTION99.88
3.03-3.070.31261350.32381617X-RAY DIFFRACTION99.89
3.07-3.120.37051410.30571645X-RAY DIFFRACTION100
3.12-3.180.34021340.27361626X-RAY DIFFRACTION99.89
3.18-3.240.31971530.26831658X-RAY DIFFRACTION99.94
3.24-3.30.30141370.2641570X-RAY DIFFRACTION100
3.3-3.360.32061390.26821665X-RAY DIFFRACTION99.94
3.36-3.440.32351420.25661594X-RAY DIFFRACTION100
3.44-3.520.30131420.22031652X-RAY DIFFRACTION100
3.52-3.610.28961410.22291591X-RAY DIFFRACTION99.94
3.61-3.70.27811450.20411631X-RAY DIFFRACTION100
3.7-3.810.23891470.20611637X-RAY DIFFRACTION99.89
3.81-3.930.20661340.19371606X-RAY DIFFRACTION100
3.93-4.080.28971470.18411630X-RAY DIFFRACTION99.94
4.08-4.240.21951400.17561644X-RAY DIFFRACTION100
4.24-4.430.18991410.16261596X-RAY DIFFRACTION100
4.43-4.660.24071410.16271631X-RAY DIFFRACTION99.94
4.66-4.950.20681430.16281628X-RAY DIFFRACTION99.77
4.96-5.340.2481480.18551622X-RAY DIFFRACTION99.61
5.34-5.870.24571410.21981601X-RAY DIFFRACTION99.77
5.87-6.710.22861420.2491633X-RAY DIFFRACTION99.72
6.72-8.440.21361310.18941615X-RAY DIFFRACTION99.94
8.45-34.750.18831370.15811609X-RAY DIFFRACTION98.37
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)
15.639882808070.1296844434830.2442822166641.20263371042-0.08030789597191.901767998380.247762717072-0.0398693849481-0.147859170478-0.132601992975-0.180497976815-0.02772145742850.3966554929890.159012658236-0.05635135266960.818222634240.054638845679-0.01167489479460.303523467189-0.004807754669890.40789916444134.4661971178-23.835176096410.2429587253
23.687555640290.8870946068471.368400861476.642766950841.23788987357.22004618288-0.087051843542-0.1619464461030.0421298931146-0.0853091059295-0.10021484102-0.1385856467760.348961799956-0.3252297922720.1848112222770.5092425177880.1113742025120.03416134885030.2634306527690.03705135063730.39350267244823.1204512623-4.038280751324.5795063243
34.090262065080.203513121034-0.06967270910090.931476993279-0.07330851722663.890707580680.2021823211130.1454864068460.368269332629-0.0377830825724-0.0880909986548-0.221480016346-0.9878390470780.0722938099653-0.1149157682320.9289012171740.1598085242970.09815756030670.349539539476-0.04057863242460.59383385468160.5935317042-31.405162667638.4927682008
44.59677507538-0.853270761688-1.294186956833.52354098080.1841276442816.341734233-0.227167907869-0.1543142768820.0417685156849-0.2890910527990.0754212047049-0.146510210941-0.0874383509298-0.3305283691620.1433373446270.5752149974610.08349934754550.07963013602930.218914281341-0.01637813393720.41549685743459.4316783358-53.56423669520.5574949788
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 3:257)AA3 - 2571 - 255
22(chain C and resseq 257:381)CB257 - 3811 - 125
33(chain E and resseq 3:257)ED3 - 2571 - 255
44(chain F and resseq 258:381)FE258 - 3811 - 124

+
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