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- PDB-6wa9: Structure of the Chlamydia pneumoniae CdsV and CdsO protein complex -

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Basic information

Entry
Database: PDB / ID: 6wa9
TitleStructure of the Chlamydia pneumoniae CdsV and CdsO protein complex
Components
  • CdsO
  • Low calcium response locus protein D
KeywordsPROTEIN TRANSPORT / Type III secretion / protein secretion / effector secretion
Function / homology
Function and homology information


protein secretion / membrane => GO:0016020 / plasma membrane
Similarity search - Function
YscO-like protein / YscO-like protein / Type III secretion protein HrcV / FHIPEP, domain 1 / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family
Similarity search - Domain/homology
Uncharacterized protein CPn0706 Homolog / Low calcium response D
Similarity search - Component
Biological speciesChlamydia pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.62 Å
AuthorsJensen, J.L. / Spiller, B.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI108778 United States
CitationJournal: Plos Pathog. / Year: 2020
Title: "The structure of the Type III secretion system export gate with CdsO, an ATPase lever arm".
Authors: Jensen, J.L. / Yamini, S. / Rietsch, A. / Spiller, B.W.
History
DepositionMar 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low calcium response locus protein D
B: Low calcium response locus protein D
C: Low calcium response locus protein D
D: Low calcium response locus protein D
E: Low calcium response locus protein D
F: Low calcium response locus protein D
G: Low calcium response locus protein D
H: Low calcium response locus protein D
I: Low calcium response locus protein D
L: CdsO
M: CdsO
N: CdsO
O: CdsO
P: CdsO
Q: CdsO
R: CdsO
S: CdsO
T: CdsO


Theoretical massNumber of molelcules
Total (without water)505,35318
Polymers505,35318
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38490 Å2
ΔGint-176 kcal/mol
Surface area188020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.410, 206.610, 280.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Low calcium response locus protein D / CdsV / Low calcium response D / Type III secretion inner membrane protein SctV


Mass: 43706.141 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia pneumoniae (bacteria)
Gene: lcrD, CP_0434, CPn_0323, BN1224_CV15_B_02600, BN1224_GiD_A_03360, BN1224_H12_DC_00060, BN1224_MUL2216_E_00600, BN1224_Panola_E_01450, BN1224_PB1_B_03220, BN1224_U1271_C_01630, BN1224_UZG1_A_ ...Gene: lcrD, CP_0434, CPn_0323, BN1224_CV15_B_02600, BN1224_GiD_A_03360, BN1224_H12_DC_00060, BN1224_MUL2216_E_00600, BN1224_Panola_E_01450, BN1224_PB1_B_03220, BN1224_U1271_C_01630, BN1224_UZG1_A_03350, BN1224_Wien2_E_01080, BN1224_YK41_BG_00210, CWL029c_C_01630
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q9Z8L5
#2: Protein
CdsO / Uncharacterized protein CPn0706 Homolog


Mass: 12444.210 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia pneumoniae (bacteria)
Gene: CPn0706 Homolog, CP_0040, CPn_0706, BN1224_CV15_C_01760, BN1224_DC9_BW_00120, BN1224_GiD_A_07350, BN1224_H12_EO_00120, BN1224_MUL2216_F_02570, BN1224_Panola_K_00310, BN1224_PB1_B_07230, BN1224_ ...Gene: CPn0706 Homolog, CP_0040, CPn_0706, BN1224_CV15_C_01760, BN1224_DC9_BW_00120, BN1224_GiD_A_07350, BN1224_H12_EO_00120, BN1224_MUL2216_F_02570, BN1224_Panola_K_00310, BN1224_PB1_B_07230, BN1224_U1271_C_05650, BN1224_UZG1_B_00310, BN1224_Wien2_G_03620, BN1224_YK41_BR_01530, CWL029c_E_00300
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q9Z7J9

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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: 4.47 Å3/Da / Density % sol: 72.48 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM Bis-Tris pH 6.0, 4% w/v PEG 3350, 200mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 4.62→52.27 Å / Num. obs: 50242 / % possible obs: 99.3 % / Redundancy: 7.5 % / CC1/2: 0.998 / Net I/σ(I): 8.1
Reflection shellResolution: 4.62→4.7 Å / Num. unique obs: 4970 / CC1/2: 0.57

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874-000refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WA6

6wa6


Resolution: 4.62→52.22 Å / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2855 2498 4.97 %
Rwork0.2408 --
obs0.243 50239 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.62→52.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29937 0 0 0 29937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00330482
X-RAY DIFFRACTIONf_angle_d0.5541236
X-RAY DIFFRACTIONf_dihedral_angle_d42.469350
X-RAY DIFFRACTIONf_chiral_restr0.0424779
X-RAY DIFFRACTIONf_plane_restr0.0055216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.62-4.710.44171390.36752636X-RAY DIFFRACTION100
4.71-4.80.38791220.36612637X-RAY DIFFRACTION100
4.81-4.910.39731490.35672608X-RAY DIFFRACTION100
4.91-5.020.35451560.322616X-RAY DIFFRACTION100
5.02-5.150.3811330.32562618X-RAY DIFFRACTION100
5.15-5.290.32541320.31872661X-RAY DIFFRACTION100
5.29-5.440.39491330.30032644X-RAY DIFFRACTION100
5.44-5.620.34591620.30672631X-RAY DIFFRACTION100
5.62-5.820.32351330.28672627X-RAY DIFFRACTION100
5.82-6.050.29331290.2732613X-RAY DIFFRACTION99
6.05-6.330.31671170.26782679X-RAY DIFFRACTION100
6.33-6.660.36891370.29062664X-RAY DIFFRACTION100
6.66-7.080.32981260.30522677X-RAY DIFFRACTION100
7.08-7.620.30011370.27732679X-RAY DIFFRACTION100
7.62-8.390.31451640.24142646X-RAY DIFFRACTION100
8.39-9.590.2281500.18662709X-RAY DIFFRACTION100
9.59-12.060.19581380.15212685X-RAY DIFFRACTION98
12.06-52.220.25731410.21662711X-RAY DIFFRACTION95
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)
13.1183-3.564-1.70955.35224.67746.4073-0.67720.5908-1.1072.4760.28860.21280.8229-0.8566-0.00173.2821-0.98650.85533.0436-0.26993.0886-16.9844-36.1466-30.146
24.131.33245.06823.6259-0.38887.4551-0.8864-0.5771-0.4078-2.09880.2410.25561.63422.48320.00244.0081-0.67631.0622.8956-0.00292.9694-19.7829-29.5665-5.3383
38.87652.44941.11944.5716-2.05641.6296-1.0886-1.0619-3.22361.1176-0.0316-0.77390.81110.4058-0.03921.68640.27581.12312.94590.55533.2984-4.3594-41.4316-0.7796
42.39691.0893-3.0341.01870.21758.23850.0302-0.3202-0.16460.4708-0.58860.4885-0.29490.09710.00062.4270.04390.12382.6866-0.15782.5648-11.58841.8938-25.9803
52.22940.3403-0.63352.2035-0.92181.4637-0.09052.0728-0.6699-0.66230.37610.47570.5144-1.30331.25570.2898-0.22430.21982.3140.03462.27789.1177-8.6514-17.2549
63.0145-0.1216-0.67650.0099-0.20853.30280.4379-0.50150.24610.4296-0.24250.4857-1.46120.4384-0.00032.91290.00370.24852.7715-0.07922.631-17.187334.9144-12.5241
75.64732.10356.20685.15622.34436.7253-0.76191.28990.6537-1.72210.9697-1.959-0.47490.85650.00931.4562-0.45150.28772.6248-0.21392.27386.932128.8012-6.4649
81.6959-0.8708-0.18932.0843-0.1479-0.02840.39070.44150.8987-1.18310.4006-0.4472-1.0746-0.1468-0.00023.15450.1120.78113.53040.16962.8131-34.480251.364815.2652
94.97850.34630.3575.65623.09725.28760.491-0.40040.28950.2522-0.42660.8629-1.81022.02490.07991.4082-1.16680.51341.82510.08741.8-9.704652.100421.7791
102.4169-2.7792-0.1944.10552.37074.66390.33270.08711.1159-1.4109-0.1194-0.8204-0.65810.3025-0.00262.3166-0.25980.68092.65240.10693.0511-61.344446.87349.6474
117.24033.18264.66768.7398-3.22038.21350.6992-0.06550.2722-0.0744-0.4448-2.0375-0.4386-0.92160.00212.2901-0.10470.6022.50250.1412.9881-35.851839.008637.4342
127.5026-5.26671.76164.81070.65613.5856-0.2908-0.2780.8228-0.43330.09790.5742-0.8992-0.5702-0.00021.9227-0.28270.22292.3095-0.31851.8931-30.32949.463154.4841
137.5773-7.8869-7.93228.09327.5389.51510.03910.612-0.4191-1.0739-0.0598-1.34640.1827-0.54770.00252.3279-0.01670.13312.3420.11072.3831-77.435410.655170.6068
145.1455-0.26080.742.47032.93373.6388-0.5255-0.0151-0.28070.22420.8705-1.19950.85251.0093-0.00012.4818-0.0170.14322.61270.18432.5091-52.752418.239457.5802
156.2498-1.3028-0.63125.318-6.52932.05380.2072-1.12842.27860.90711.18490.3798-1.6217-2.41670.52811.5748-0.4667-0.36062.3393-0.38161.1267-44.601221.927777.6748
164.66910.3079-3.99481.65482.43127.71090.31781.10771.23180.56450.2833-1.1234-0.3405-0.8831-0.00252.8920.08330.70352.34940.11143.2804-70.9794-31.796762.2325
179.34317.4364-6.02555.9-4.78293.84350.1996-0.8937-0.58070.3453-0.89150.0968-0.46390.71440.00152.58830.10150.33412.6551-0.02362.6605-61.7907-17.623463.5177
185.9133-3.1275-0.6465.141-1.60615.8597-0.05370.34880.50241.01480.33750.8095-0.3236-1.08-0.00020.95160.1362-0.05491.86190.04921.8418-47.2835-13.784877.4511
191.0221.13620.72834.8667-1.2911.3421-0.76320.259-0.3444-1.50550.6083-1.46580.308-0.2517-0.00042.49670.08210.49312.6435-0.08112.6963-51.8936-52.123440.4581
206.7272.90192.69389.95152.19883.4347-0.07860.6385-0.21161.76740.4951.06650.2365-0.31830.00091.28210.39630.39022.28870.25562.49-36.5377-44.621460.2885
216.62345.49620.73618.281-1.67784.9850.14911.36971.17560.6685-0.5946-0.302-1.0738-1.3157-0.20992.4945-0.17391.42982.97890.15222.5989-33.8568-56.1283-1.7211
221.3105-0.57750.10931.28211.9133.63840.16860.6330.6436-2.1954-0.1951-2.1955-0.8569-0.5249-1.83691.9951-0.73461.46012.8914-0.37842.631-32.51-64.99438.6117
236.9114-7.7505-1.74148.63242.06435.05840.3436-1.02740.2296-1.6121-0.9432-0.94-0.9187-0.0025-0.94681.3930.03020.4012.52980.15032.4532-29.3619-45.168828.5582
248.994-0.76220.80695.5187-2.60546.9475-0.11650.0678-0.0426-0.65770.21240.48450.13030.80960.00110.90770.42660.39182.69130.10162.6843-14.2302-57.225329.7046
259.46044.36782.58492.02091.18140.6792-2.1444-1.59417.5677-0.71650.32681.07-0.6625-0.3592-0.03784.9520.0595-0.99293.40440.22965.8726-13.887-29.150584.5932
268.6031-7.1386-2.55115.92922.11550.712-0.4505-4.20946.2865-0.76990.338-1.3985-4.0507-1.19270.40153.0041-0.260.02033.91670.29112.308-20.3918-28.172975.4043
272.9259-0.99710.944.59771.6351.16322.8045-5.75972.20762.0287-2.6008-0.4513-0.8083-1.74560.00283.7719-1.2166-0.91064.7105-0.24034.1541-30.13332.218190.8051
283.41362.43240.8531.71820.60510.1902-2.7539-2.01761.914-0.90760.9511-1.3444-0.9388-0.7980.00172.48340.45140.30023.867-0.23073.6047-26.62371.696781.9584
291.015-2.29971.60645.3577-3.70792.47124.7756-0.19633.0152-1.6361-3.0847-0.14030.74210.43020.08353.3852-0.7121-0.29714.385-0.26874.2343-13.759636.044579.0837
303.18793.686-2.13074.789-2.79251.6056-4.4941-1.47790.4757-1.42551.6146-0.8993-1.24880.3705-0.00294.27840.6393-0.04653.08810.09663.5319-13.426329.096273.9979
311.5931-0.8741-0.06623.67193.78284.3678-3.8774-3.1878-0.43954.37951.0038-1.57793.8322-0.9875-0.32734.789-0.1879-0.08734.77470.3194.6376-2.48154.249150.0768
328.5332-7.6542-1.40487.96132.65381.9083-3.50222.00730.9806-2.90961.2488-1.81382.7343-0.15691.38467.702-1.49730.40274.13621.45543.8239-1.646744.570949.7104
332.7431-2.94262.61523.424-2.72142.5120.36514.05341.63233.2196-1.6082-3.0051-1.07821.6114-0.10633.6484-1.0858-0.21125.9599-0.35224.762816.013941.933517.4615
340.06510.6222-0.14565.2854-1.38270.3533-3.78158.01550.734-3.48610.4737-5.638-1.5446.065-2.244.4785-1.95980.1067.6716-0.76374.876811.379234.147320.4823
351.14090.50791.72431.45171.34782.8345-2.62511.45750.8156-0.695-2.0285-4.17380.77070.39150.00382.2406-0.59440.30664.36370.99754.560627.987810.5209-1.7722
362.00817.91329.06675.50926.32477.27775.08231.62-4.94390.8577-1.7062-1.01893.75281.95933.18454.023-0.83380.68295.3673-0.03822.747922.46197.88535.757
371.2705-0.76910.50990.5602-0.2690.2073-2.2842-2.02864.06220.69080.948-0.29992.7699-0.44630.00112.7701-0.47480.19995.4002-0.28994.19422.4161-25.9809-6.4673
389.07568.96139.05298.81788.91829.01762.077-2.7978-1.8871.8966-1.4157-0.042.8375-2.819-3.80641.6288-0.6499-0.2894.0191-0.84712.753218.8479-22.87344.2395
395.4061-6.8223-8.33948.606621.99790.51821.2038-2.6996-1.8902-3.01337.72082.7777-5.4047-0.71435.23920.8256-0.04462.39-0.21363.85378.8516-55.067215.7755
404.5822-4.77062.38825.3944-1.59413.093-1.45491.01270.68621.0964-0.66741.2310.8849-2.45612.80253.3952-1.8322-0.67543.54530.46346.0379-2.0898-51.077114.2018
410.18660.34030.60751.05531.181.83631.1899-0.58310.1966-0.7301-0.68880.62782.04941.3423-0.0063.4050.1513-0.17325.27810.49293.6362-2.4569-50.868359.8992
422.40990.65512.11541.7647-0.50612.5183-0.3882-3.3241-0.35161.0855-0.6796-2.4645-1.0242-0.15730.00032.4623-0.5132-0.6353.72610.33444.2169-8.2194-46.258452.6153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 364 through 497 )
2X-RAY DIFFRACTION2chain 'A' and (resid 498 through 560 )
3X-RAY DIFFRACTION3chain 'A' and (resid 561 through 700 )
4X-RAY DIFFRACTION4chain 'B' and (resid 362 through 594 )
5X-RAY DIFFRACTION5chain 'B' and (resid 595 through 709 )
6X-RAY DIFFRACTION6chain 'C' and (resid 362 through 603 )
7X-RAY DIFFRACTION7chain 'C' and (resid 604 through 708 )
8X-RAY DIFFRACTION8chain 'D' and (resid 363 through 604 )
9X-RAY DIFFRACTION9chain 'D' and (resid 605 through 708 )
10X-RAY DIFFRACTION10chain 'E' and (resid 362 through 532 )
11X-RAY DIFFRACTION11chain 'E' and (resid 533 through 612 )
12X-RAY DIFFRACTION12chain 'E' and (resid 613 through 708 )
13X-RAY DIFFRACTION13chain 'F' and (resid 364 through 497 )
14X-RAY DIFFRACTION14chain 'F' and (resid 498 through 612 )
15X-RAY DIFFRACTION15chain 'F' and (resid 613 through 709 )
16X-RAY DIFFRACTION16chain 'G' and (resid 362 through 461 )
17X-RAY DIFFRACTION17chain 'G' and (resid 462 through 579 )
18X-RAY DIFFRACTION18chain 'G' and (resid 580 through 710 )
19X-RAY DIFFRACTION19chain 'H' and (resid 362 through 579 )
20X-RAY DIFFRACTION20chain 'H' and (resid 580 through 705 )
21X-RAY DIFFRACTION21chain 'I' and (resid 362 through 451 )
22X-RAY DIFFRACTION22chain 'I' and (resid 452 through 532 )
23X-RAY DIFFRACTION23chain 'I' and (resid 533 through 616 )
24X-RAY DIFFRACTION24chain 'I' and (resid 617 through 708 )
25X-RAY DIFFRACTION25chain 'L' and (resid 23 through 65 )
26X-RAY DIFFRACTION26chain 'L' and (resid 66 through 105 )
27X-RAY DIFFRACTION27chain 'M' and (resid 36 through 68 )
28X-RAY DIFFRACTION28chain 'M' and (resid 69 through 100 )
29X-RAY DIFFRACTION29chain 'N' and (resid 25 through 68 )
30X-RAY DIFFRACTION30chain 'N' and (resid 69 through 110 )
31X-RAY DIFFRACTION31chain 'O' and (resid 33 through 68 )
32X-RAY DIFFRACTION32chain 'O' and (resid 69 through 106 )
33X-RAY DIFFRACTION33chain 'P' and (resid 36 through 68 )
34X-RAY DIFFRACTION34chain 'P' and (resid 69 through 100 )
35X-RAY DIFFRACTION35chain 'Q' and (resid 34 through 68 )
36X-RAY DIFFRACTION36chain 'Q' and (resid 69 through 104 )
37X-RAY DIFFRACTION37chain 'R' and (resid 42 through 68 )
38X-RAY DIFFRACTION38chain 'R' and (resid 69 through 100 )
39X-RAY DIFFRACTION39chain 'S' and (resid 45 through 65 )
40X-RAY DIFFRACTION40chain 'S' and (resid 66 through 84 )
41X-RAY DIFFRACTION41chain 'T' and (resid 28 through 65 )
42X-RAY DIFFRACTION42chain 'T' and (resid 66 through 102 )

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