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- PDB-9dcr: Structure of the TelA-associated type VII secretion system chaper... -

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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 / homologyProtein of unknown function DUF4176 / Domain of unknown function (DUF4176) / DUF4176 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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

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

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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

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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

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