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- PDB-9dct: Structure of the TelB-associated type VII secretion system chaper... -

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Basic information

Entry
Database: PDB / ID: 9dct
TitleStructure of the TelB-associated type VII secretion system chaperone SIR_0178
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: 3.24 Å
AuthorsGkragkopoulou, P. / 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
C: DUF4176 domain-containing protein
D: DUF4176 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5235
Polymers115,4884
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-101 kcal/mol
Surface area42140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.808, 69.848, 253.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
DUF4176 domain-containing protein


Mass: 28871.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius B196 (bacteria)
Gene: SIR_0178 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1ZCG6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M NaCl, 0.1M Tris:HCl pH 8.5, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.24→50 Å / Num. obs: 18608 / % possible obs: 94.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 126.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.045 / Rrim(I) all: 0.172 / Net I/σ(I): 17.6
Reflection shellResolution: 3.24→3.31 Å / Redundancy: 10.3 % / Rmerge(I) obs: 2.296 / Mean I/σ(I) obs: 1 / Num. unique obs: 849 / CC1/2: 0.767 / Rpim(I) all: 0.65 / Rrim(I) all: 2.393 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→46.34 Å / SU ML: 0.6125 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.6406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3084 937 5.09 %
Rwork0.2588 17463 -
obs0.2614 18400 92.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 148.35 Å2
Refinement stepCycle: LAST / Resolution: 3.24→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 1 0 7321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00157490
X-RAY DIFFRACTIONf_angle_d0.415710167
X-RAY DIFFRACTIONf_chiral_restr0.03811143
X-RAY DIFFRACTIONf_plane_restr0.00331292
X-RAY DIFFRACTIONf_dihedral_angle_d13.29322748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.410.37571140.41892077X-RAY DIFFRACTION78.84
3.41-3.620.50071270.37192403X-RAY DIFFRACTION90.1
3.62-3.90.43951060.33762477X-RAY DIFFRACTION91.53
3.9-4.290.32681440.30022437X-RAY DIFFRACTION91.92
4.29-4.910.31851440.25552540X-RAY DIFFRACTION93.88
4.91-6.190.32811440.26432708X-RAY DIFFRACTION98.89
6.19-46.340.24841580.20752821X-RAY DIFFRACTION98.12
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)
11.899922069930.5178145457370.09203502604423.958017711361.791239962744.77622274441-0.0560002622863-0.0229016111846-0.316993262622-0.204853775105-0.2671407525480.6290210466140.754935395078-1.202337459860.2694169188651.13081926073-0.252780648223-0.02955917200551.38020890713-0.07392598561141.09472159253-22.6892235308-27.5384338202-43.4578952668
25.81819380992.01687919975-0.5759742902771.019584127591.636371448645.85163313873-0.447020194877-0.117750319663-0.126960355686-0.2220292038410.023302561319-0.367515620906-0.291190344213-0.09351830919610.4469623837840.961272570129-0.0478359689417-0.02401952682490.8858974933220.09109548875821.09822937528-8.00414081084-16.5393168552-39.4647955223
34.38301992561.219414549532.715802591795.24801017462-1.695373876073.09504724230.4151607538060.333127568542-0.519422126763-0.455971808206-0.591907849837-8.6242430896E-52.19599305275-0.4011739031250.2135592856621.78613079054-0.0493087819933-0.1022689844771.12837773281-0.02471532887741.2025076122-9.80137797884-26.6374664952-32.9410556688
44.804377701623.72012042135-0.3100818520352.683432965380.08204466155517.58214689095-0.001233049008480.100365555384-0.09832708378240.6794838537010.319126840331-0.5318779757540.2947115172840.443686344901-0.135104685111.054936324590.234445585651-0.1582232971520.896117411755-0.08104007768771.2967228545221.6018025595-31.4557332419-9.47233606205
50.288749082247-0.181043463024-1.066523065715.51623795786-1.380718812852.024853884710.2554045645530.2743339820220.203553294540.288829340662-0.300606600229-1.376968727160.240046305840.64907131318-0.1399788369810.9738235100090.153723551365-0.1691030559470.998334866144-0.146472970811.0345118093217.7267929626-21.0805730134-16.8418547971
65.62955783218-0.446392541722-1.681669582081.37763555309-2.220533041394.606476489230.2968753767970.06335067379760.342805016088-0.49636077427-0.09122135231320.0721765894089-1.24567300919-0.1716208690490.2064815656091.00952484503-0.0739113469548-0.05280151084510.7037027582170.08847826015230.9590142444618.66063966721-15.2068488442-21.7364912463
74.87766787159-0.169338083304-1.068068100622.33882019715-0.4513539348359.686628584660.4396248110750.123610426301-0.0308027949075-0.273410232238-0.295943757597-0.0315546127160.270212609226-0.04290866292450.3615339514591.348183687180.178757679865-0.01474051728390.9845547234410.08395599612961.388126338477.83291835076-26.8488138925-23.3821547948
84.322515056520.609533256353-0.3527615728996.73947779156-2.404332323235.920092670940.659161697169-0.03790611497730.367520683091-0.286050580313-0.628195788168-0.631968763770.4353688738791.468851659880.02017627557180.856743822474-0.09005908986650.09412384059851.458082723450.07172588956811.1925964762823.83233617295.88336774714-56.2407286867
90.5340884264194.49378556067-2.663695734213.0202001473-3.162420818935.06144163365-0.6632652968270.8210192926570.61624168434-0.5352542404570.693357330938-0.0209762050748-0.6839305215960.0219462466216-0.4284993475391.034258387150.0385979258585-0.05238513715241.200414103770.1240114165191.3173344190316.64982770720.122221528666-47.4912927763
102.87577252028-1.960713637292.101554481493.47334118717-0.355803547187.768370777350.3235763668980.2969960238250.043350326996-0.971464535016-0.0666835175656-0.3836010474170.576634878145-0.0172446760963-0.1285235941490.9683025687910.0512753275160.2502471160661.182635195160.1108998566661.27079447595.97889701151-4.38771741129-45.8277542696
112.943726801271.244382734411.22540434814.91627852512-0.1698992358732.311271258980.3223563230650.1375976460610.134174321168-0.00153080729033-0.395326158615-0.428769300607-0.1272562224540.7016160183840.01927316564891.22798702489-0.1623569647560.1505743099071.200124568940.1395733312871.3618737085117.95279673094.84417114356-32.1039024756
124.206243719263.448938633970.9259456684836.332448673160.3565080366894.683906616840.5162375664580.7950462850880.5575125576620.746873479740.252149393753-0.115975016418-1.40512228411-0.741379679355-0.7334027224832.343558946840.658294860430.5452729913611.25555303680.2377425618611.73556913434-20.175482986815.9289731274-15.4566246188
134.866896591771.112079319361.344425078670.1235236715330.8594933397336.296771878980.3134721951470.688815579970.750204235139-0.623578397751-0.2129440862530.314409457538-1.00753348255-0.65593196609-0.3190322378831.397615009130.06317556534820.2437124516220.632026261161-0.05940369828631.37294599763-10.048455732-0.639927715314-21.6380544377
141.814362431980.9715389141180.3868037197810.255507437686-0.4680315154195.409793392820.1181596302420.07331647908880.4783093185690.8224420087070.3381205663620.31432948117-1.78300766248-0.373103909423-0.2841750609181.292511744030.1064293921190.2386950842830.8219657682890.0184204769341.29068618996-6.073414723512.74642418099-24.3382178799
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 141)AA2 - 1411 - 138
22chain 'A' and (resid 142 through 189 )AA142 - 189139 - 186
33chain 'A' and (resid 190 through 231 )AA190 - 231187 - 228
44chain 'B' and (resid 1 through 82)BB1 - 821 - 82
55chain 'B' and (resid 83 through 141)BB83 - 14183 - 137
66chain 'B' and (resid 142 through 189 )BB142 - 189138 - 185
77chain 'B' and (resid 190 through 229 )BB190 - 229186 - 225
88chain 'C' and (resid 1 through 82)CC1 - 821 - 82
99chain 'C' and (resid 83 through 148 )CC83 - 14883 - 137
1010chain 'C' and (resid 149 through 205)CC149 - 205138 - 194
1111chain 'C' and (resid 206 through 232 )CC206 - 232195 - 221
1212chain 'D' and (resid 1 through 102 )DD1 - 1021 - 102
1313chain 'D' and (resid 103 through 158 )DD103 - 158103 - 156
1414chain 'D' and (resid 159 through 230 )DD159 - 230157 - 228

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