[English] 日本語
Yorodumi
- PDB-9dcr: Structure of the TelA-associated type VII secretion system chaper... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dcr
TitleStructure of the TelA-associated type VII secretion system chaperone SIR_0168
ComponentsDUF4176 domain-containing protein
KeywordsCHAPERONE / Molecular chaperone / type vii secretion system / antibacterial toxins
Function / homologyDUF4176 domain-containing protein
Function and homology information
Biological speciesStreptococcus intermedius B196 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGrebenc, D.W. / Kim, Y. / Whitney, J.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-173486 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: A widespread family of molecular chaperones promotes the intracellular stability of type VIIb secretion system-exported toxins.
Authors: Gkragkopoulou, P. / Garrett, S.R. / Shah, P.Y. / Grebenc, D.W. / Klein, T.A. / Kim, Y. / Whitney, J.C.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUF4176 domain-containing protein
B: DUF4176 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2869
Polymers53,9582
Non-polymers3287
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-49 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.760, 63.490, 111.990
Angle α, β, γ (deg.)90.000, 101.550, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein DUF4176 domain-containing protein


Mass: 26978.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius B196 (bacteria)
Gene: SIR_0168 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1ZCF9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 200mM Sodium Thiocyanate pH 6.9, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→45.24 Å / Num. obs: 36953 / % possible obs: 95.5 % / Redundancy: 8.3 % / Biso Wilson estimate: 34.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.015 / Rrim(I) all: 0.043 / Net I/σ(I): 24.5
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1341 / CC1/2: 0.95 / Rpim(I) all: 0.168 / Rrim(I) all: 0.449 / % possible all: 69.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→39.88 Å / SU ML: 0.236 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 28.4403
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2444 1778 4.81 %
Rwork0.1947 35162 -
obs0.1967 36940 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.32 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 16 118 3639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033680
X-RAY DIFFRACTIONf_angle_d0.56374995
X-RAY DIFFRACTIONf_chiral_restr0.0446560
X-RAY DIFFRACTIONf_plane_restr0.0041639
X-RAY DIFFRACTIONf_dihedral_angle_d15.13381379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.40461050.31732056X-RAY DIFFRACTION72.74
1.9-1.960.29471320.25752447X-RAY DIFFRACTION88.5
1.96-2.020.25661220.2262760X-RAY DIFFRACTION97.3
2.02-2.090.25471580.22362742X-RAY DIFFRACTION97.64
2.09-2.170.29391460.22372793X-RAY DIFFRACTION98.16
2.18-2.270.27241670.21562705X-RAY DIFFRACTION97.06
2.27-2.390.2651380.20972787X-RAY DIFFRACTION98.55
2.39-2.540.24131700.20882764X-RAY DIFFRACTION98.59
2.54-2.740.27111580.22292754X-RAY DIFFRACTION98.01
2.74-3.020.2781230.21232805X-RAY DIFFRACTION98.82
3.02-3.450.25291500.19382812X-RAY DIFFRACTION98.8
3.45-4.350.2071110.16932820X-RAY DIFFRACTION98.45
4.35-39.880.2087980.17572917X-RAY DIFFRACTION97.83
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)
13.984542431691.22346372574-1.122893817653.173922609571.018810533116.35238458406-0.1296450455410.0386178181126-0.00290240585989-0.1598092507760.145747885057-0.149940583064-0.04244811030890.6799392875850.06387557313850.2866198834450.0486418374672-0.000336693234650.4856278354060.007870827472210.29644129745716.724320492113.70364597289.04479035674
23.82435149048-0.245414247631-1.017274521841.09729789270.2582087131572.63335338482-0.01971720935310.231529411264-0.137578373156-0.0407611493623-0.0415718981985-0.05009759935580.243252321990.2543165484590.03407387655730.3320835720220.0522513867177-0.006401629001870.269812708241-0.04404621771920.284925456971-1.1783331484111.427576875221.3076853535
30.940193214419-0.197369791758-0.6209489599642.15410083413-0.7608628422266.560920174880.1033416930830.442882331545-0.0205994450852-0.09264340157640.02119156062830.0722654730569-0.448721247729-0.742755367925-0.03639575624790.3334369291950.04324870443120.03675792864610.3480669568220.01684301729280.338202611618-34.494782254924.975383367639.8273998166
42.20173420239-0.685370071308-0.4541397880812.670926885841.303677693980.6470925541390.339378902446-0.565929250890.602076790808-0.447660613101-0.0955775376679-0.35871681017-0.7154567821470.387540819205-0.1653906768010.660819956195-0.05116979175070.1025626261030.464934275868-0.0754402905430.499961311295-27.709245064530.772690123750.7041161674
52.82318328051-0.660210475016-0.5574793543260.4986987453440.2049924062992.330361599620.0795230984154-0.400920146241-0.06991071270650.1432878239670.0327605471290.00830938670426-0.04440134083020.0311331501431-0.1205006701910.352286974029-0.0161679684511-0.007875025842590.250286740020.001045539663270.32698864918-22.983926605621.157650475545.177170626
64.70610067328-0.191201795564-1.357687705181.034295367050.4957056129554.54727764119-0.1141900572950.157975979527-0.611193818970.03433855236-0.03318706717560.1307269681810.407885894531-0.1552895019680.03803695048030.3309389502290.0137901927371-0.005791567717640.0953727711162-0.05241659718190.346663217537-19.614983008714.238643765833.8152150384
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 101 )AA1 - 1012 - 102
22chain 'A' and (resid 102 through 214 )AA102 - 214103 - 215
33chain 'B' and (resid 1 through 47 )BH1 - 471 - 47
44chain 'B' and (resid 48 through 62 )BH48 - 6248 - 62
55chain 'B' and (resid 63 through 140 )BH63 - 14063 - 140
66chain 'B' and (resid 141 through 214 )BH141 - 214141 - 214

+
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