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- PDB-6wa6: Structure of the Chlamydia pneumoniae CdsV protein -

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Basic information

Entry
Database: PDB / ID: 6wa6
TitleStructure of the Chlamydia pneumoniae CdsV protein
ComponentsLow 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
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
Low calcium response D
Similarity search - Component
Biological speciesChlamydia pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 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 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,55222
Polymers393,3559
Non-polymers1,19713
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24130 Å2
ΔGint-78 kcal/mol
Surface area149550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.650, 280.440, 290.410
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.45 Å3/Da / Density % sol: 64.35 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.75 / Details: 100 mM HEPES pH 6.75, 5% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→126.27 Å / Num. obs: 134510 / % possible obs: 99.4 % / Redundancy: 6 % / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 13227 / CC1/2: 0.718

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→126.27 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.24
RfactorNum. reflection% reflection
Rfree0.2442 6708 4.99 %
Rwork0.1959 --
obs0.1983 134496 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→126.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24779 0 78 58 24915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925455
X-RAY DIFFRACTIONf_angle_d1.09234525
X-RAY DIFFRACTIONf_dihedral_angle_d20.7369784
X-RAY DIFFRACTIONf_chiral_restr0.0623994
X-RAY DIFFRACTIONf_plane_restr0.0084337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.34162050.31114094X-RAY DIFFRACTION98
2.83-2.870.34372480.29374209X-RAY DIFFRACTION100
2.87-2.90.35232420.29124229X-RAY DIFFRACTION100
2.9-2.940.31462290.27974134X-RAY DIFFRACTION99
2.94-2.980.34612210.27264233X-RAY DIFFRACTION100
2.98-3.020.30352010.26674300X-RAY DIFFRACTION100
3.02-3.060.34862150.26894188X-RAY DIFFRACTION99
3.06-3.10.35392460.29074200X-RAY DIFFRACTION100
3.11-3.150.31462140.27124269X-RAY DIFFRACTION100
3.15-3.210.31922360.25064197X-RAY DIFFRACTION100
3.21-3.260.27512050.23424232X-RAY DIFFRACTION100
3.26-3.320.26322390.22444248X-RAY DIFFRACTION100
3.32-3.380.26982270.22674205X-RAY DIFFRACTION100
3.38-3.450.28592320.21944245X-RAY DIFFRACTION100
3.45-3.530.28682220.21544267X-RAY DIFFRACTION100
3.53-3.610.26512290.20984202X-RAY DIFFRACTION100
3.61-3.70.27712510.22154302X-RAY DIFFRACTION100
3.7-3.80.27072180.20954175X-RAY DIFFRACTION100
3.8-3.910.23482260.18544325X-RAY DIFFRACTION100
3.91-4.040.21951950.19034249X-RAY DIFFRACTION100
4.04-4.180.23832280.17714280X-RAY DIFFRACTION99
4.18-4.350.20822120.16074255X-RAY DIFFRACTION100
4.35-4.550.19532380.14914269X-RAY DIFFRACTION99
4.55-4.790.21512410.15624298X-RAY DIFFRACTION99
4.79-5.090.18882080.15564304X-RAY DIFFRACTION99
5.09-5.480.20562010.15844305X-RAY DIFFRACTION99
5.48-6.030.22142140.17214348X-RAY DIFFRACTION99
6.03-6.90.26262280.19944311X-RAY DIFFRACTION99
6.91-8.70.21072050.1774354X-RAY DIFFRACTION98
8.7-126.270.2032320.17814562X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5398-0.45960.43822.6104-0.11721.4668-0.1067-0.1019-0.1974-0.02060.1472-0.18360.18240.0935-0.02080.34150.02710.08830.33250.0090.394325.8629-44.7806-2.5778
26.92811.9782-1.65536.5851-0.67897.67950.0323-0.54970.00330.36110.14970.7719-0.0065-0.1767-0.05450.3948-0.09790.09830.380.03120.5276-1.1579-47.4585-5.9953
33.8097-1.15691.6125.0658-1.61655.9577-0.4114-0.6198-0.23181.13340.2977-0.2505-0.04660.38270.04260.53270.0659-0.070.58660.02340.467439.1583-17.065630.6759
42.46690.8816-0.30764.02681.25975.6755-0.3255-0.20460.0165-0.14490.01290.1275-0.0971-0.21730.24930.23780.0467-0.07860.3383-0.0430.418519.9981-20.41626.8517
57.5624-1.0391-2.94466.10742.45246.2957-0.3763-1.3494-0.25520.5070.02050.57620.057-0.30040.33330.42340.03830.18170.8343-0.18760.58466.1882-22.36122.7305
62.3155-0.7748-0.32992.2136-0.32725.4166-0.3866-0.21890.34010.3109-0.1083-0.94790.07990.9280.36380.844-0.1926-0.22810.74810.07560.815147.751424.25316.6671
73.1461-0.94630.63893.2995-0.68962.4627-0.5326-0.83870.32820.75450.18330.2194-0.55790.15490.17860.78180.0012-0.07040.6512-0.02150.365834.278517.987321.1154
86.42510.75673.43252.97910.28096.1886-0.7582-1.33490.89260.79760.55640.885-2.014-0.52420.21931.44860.51260.29841.16790.14181.05669.824718.045726.901
95.4469-0.64591.69334.7680.67170.70160.2071-1.4988-0.611.07320.24820.3121-1.3899-1.1390.07241.46310.31360.58590.9630.1111.0316.979413.720929.4847
103.87162.29510.64634.44680.26464.63110.03760.1259-0.1287-0.1687-0.0064-0.6527-0.29030.6395-0.06840.6704-0.1450.08090.511-0.03450.57150.276949.7926-10.7287
111.34781.05640.4493.38990.57952.06170.0096-0.12630.0978-0.00790.0201-0.0908-0.2139-0.0114-0.0170.5211-0.07280.01080.4059-0.02260.407637.289745.8309-0.9309
124.1847-2.90821.60459.0999-0.6246.9779-0.0003-0.66540.68150.9053-0.06790.8871-0.3944-0.58760.06610.66480.1110.2530.7278-0.10450.755215.604247.86236.9678
132.10921.7668-0.18163.4616-0.59191.1907-0.41410.35020.5143-0.52130.41770.0506-1.23140.6422-0.04341.7622-0.44980.05940.85790.02650.744.62461.2806-46.8583
141.98090.5961.03512.7489-0.183.53670.0725-0.00780.1297-0.52790.03240.0677-0.2534-0.1418-0.11290.7011-0.02630.04230.4396-0.0790.350527.987644.5013-27.1411
156.2335-2.0332.08543.7322-2.42016.21490.1970.24560.3807-1.2208-0.2910.681-0.5837-0.61750.09011.15510.3416-0.21490.6031-0.09980.667315.03860.7807-29.9474
165.99653.0571-4.46171.6801-2.60988.00420.20780.2281-0.5175-0.6094-0.1529-0.62710.39160.87650.52451.733-0.1750.41110.8804-0.18330.485442.174920.1602-79.8134
172.7383-0.171-1.33850.7757-1.70315.04670.06250.3287-0.0107-0.91780.26-0.4478-0.34650.5055-0.23661.7529-0.3020.29570.7801-0.07480.612340.789531.253-79.3541
185.2755-6.16194.29047.2065-5.07283.7037-0.23340.4590.0239-1.11260.29630.87270.11510.21960.13122.0507-0.4962-0.0271.11690.21090.839232.964246.3834-93.3615
190.62290.3593-1.27950.2457-0.8152.6495-0.42040.29520.303-1.06780.3347-0.3032-0.11860.0229-0.00061.7094-0.31450.12390.7420.02660.634136.97736.8983-74.9324
203.7190.9250.62375.2574-0.08444.1165-0.17260.16810.6037-0.42110.08040.7337-0.6404-0.61690.0751.0231-0.0182-0.07960.5305-0.06280.529423.126738.4905-54.2186
218.42465.6792-5.45847.0726-0.34787.48590.39120.47080.6622-1.4083-0.47791.45570.2033-1.72340.31710.89240.209-0.42331.38530.15981.45361.565742.1539-65.9207
223.35562.7101-1.26292.6090.72646.8502-0.2230.61331.7259-0.538-0.05950.7831-0.1148-1.0963-0.07531.67430.1149-0.42861.55930.69761.043415.224949.6188-70.9323
234.8105-0.8791-1.3354.7262-0.85265.0976-0.23090.38940.3358-1.0270.59970.3895-1.9005-1.001-0.40741.4690.1306-0.67170.7699-0.01761.091915.350548.1752-64.3586
242.27810.0987-3.07511.8942-0.78257.0409-0.06360.3559-0.0254-0.00490.0937-0.15530.8618-0.0133-0.0531.0566-0.06480.06610.6814-0.01020.471132.0448-4.8369-89.3232
254.2918-0.19692.31142.42190.50275.7261-0.1944-0.00610.248-0.21390.01520.1072-0.1869-0.350.17081.1302-0.13620.01780.5051-0.02520.423619.802913.2445-67.9767
267.61350.27112.64124.2515-0.60697.79130.46520.922-0.3807-0.7172-0.29970.2467-0.2639-0.379-0.16471.1777-0.0693-0.23430.8815-0.03360.49027.535913.5027-86.8703
272.527-0.29292.01122.14930.7791.9779-0.18040.1754-0.4751-0.39970.3675-0.59590.37481.22630.05052.06760.15340.34940.79440.04610.661128.7562-40.1653-66.598
280.70910.0074-0.87670.0092-0.00551.0760.0975-0.0523-0.8608-0.2946-0.67630.42441.59060.32560.20112.86980.09740.17080.704-0.04770.846920.3542-50.4285-69.0469
291.1626-0.1924-0.96670.68431.6024.02150.48570.3741-0.509-0.9942-0.90490.67510.4858-0.25260.37272.61240.2108-0.03550.8663-0.20430.892317.631-44.8849-82.8922
303.92150.6059-1.94263.9199-0.98387.8059-0.08380.44880.1045-0.16060.14890.34060.3834-0.5776-0.05331.2226-0.1883-0.03250.53750.05050.470715.8434-14.2224-63.8502
316.48710.65570.67892.77581.8631.2483-0.49191.75160.0417-1.76150.6720.411-0.0306-0.7080.00051.4149-0.5612-0.73671.73850.09480.8736-5.4038-23.0387-79.3213
325.96840.78760.02665.85061.38470.32850.13780.797-0.1627-1.27480.14171.01310.7714-1.6753-0.04151.1778-0.4705-0.39281.490.23260.90481.0475-21.6872-77.7293
332.593-0.9819-1.43552.5913.46534.586-0.1498-0.2314-0.5718-0.0770.1603-0.47660.91820.6977-0.22660.87560.18920.06770.61960.05750.548931.0497-54.0444-23.1438
343.69110.57360.37413.23572.882.5886-0.28210.1629-0.0442-0.93550.1839-1.07010.74750.63620.03991.22470.10720.31950.6123-0.01820.671328.8071-55.7096-35.3869
351.55230.1901-0.12454.09672.91182.0705-0.10040.2888-0.762-0.5986-0.01080.14410.58570.01730.07371.4814-0.00470.2560.5308-0.10570.859820.3683-68.9803-37.4703
361.9751-0.59060.5924.2082-0.74264.6192-0.14280.1462-0.008-0.77530.14590.41750.0673-0.11550.02251.0327-0.10520.00820.45690.04350.434313.2046-33.4568-43.7595
374.3269-0.0485-1.56843.3755-0.86230.85850.18880.2613-0.7638-1.44540.15890.551.2451-1.1802-0.06850.9934-0.7831-0.31371.43930.16491.1987-6.8756-48.0604-44.939
388.02520.9870.41925.1441.78982.4383-0.0529-0.2108-0.7573-1.4043-0.02470.87011.1746-1.454-0.06181.3235-0.4982-0.35941.19360.12260.9113-1.6111-48.5282-50.2796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 363 through 603 )
2X-RAY DIFFRACTION2chain 'A' and (resid 604 through 710 )
3X-RAY DIFFRACTION3chain 'B' and (resid 363 through 512 )
4X-RAY DIFFRACTION4chain 'B' and (resid 513 through 616 )
5X-RAY DIFFRACTION5chain 'B' and (resid 617 through 709 )
6X-RAY DIFFRACTION6chain 'C' and (resid 361 through 420 )
7X-RAY DIFFRACTION7chain 'C' and (resid 421 through 603 )
8X-RAY DIFFRACTION8chain 'C' and (resid 604 through 653 )
9X-RAY DIFFRACTION9chain 'C' and (resid 654 through 709 )
10X-RAY DIFFRACTION10chain 'D' and (resid 363 through 429 )
11X-RAY DIFFRACTION11chain 'D' and (resid 430 through 603 )
12X-RAY DIFFRACTION12chain 'D' and (resid 604 through 708 )
13X-RAY DIFFRACTION13chain 'E' and (resid 363 through 512 )
14X-RAY DIFFRACTION14chain 'E' and (resid 513 through 616 )
15X-RAY DIFFRACTION15chain 'E' and (resid 617 through 708 )
16X-RAY DIFFRACTION16chain 'F' and (resid 363 through 385 )
17X-RAY DIFFRACTION17chain 'F' and (resid 386 through 452 )
18X-RAY DIFFRACTION18chain 'F' and (resid 453 through 477 )
19X-RAY DIFFRACTION19chain 'F' and (resid 478 through 532 )
20X-RAY DIFFRACTION20chain 'F' and (resid 533 through 616 )
21X-RAY DIFFRACTION21chain 'F' and (resid 617 through 649 )
22X-RAY DIFFRACTION22chain 'F' and (resid 650 through 672 )
23X-RAY DIFFRACTION23chain 'F' and (resid 673 through 707 )
24X-RAY DIFFRACTION24chain 'G' and (resid 364 through 532 )
25X-RAY DIFFRACTION25chain 'G' and (resid 533 through 603 )
26X-RAY DIFFRACTION26chain 'G' and (resid 604 through 709 )
27X-RAY DIFFRACTION27chain 'H' and (resid 362 through 420 )
28X-RAY DIFFRACTION28chain 'H' and (resid 421 through 452 )
29X-RAY DIFFRACTION29chain 'H' and (resid 453 through 517 )
30X-RAY DIFFRACTION30chain 'H' and (resid 518 through 603 )
31X-RAY DIFFRACTION31chain 'H' and (resid 604 through 650 )
32X-RAY DIFFRACTION32chain 'H' and (resid 651 through 703 )
33X-RAY DIFFRACTION33chain 'I' and (resid 362 through 385 )
34X-RAY DIFFRACTION34chain 'I' and (resid 386 through 429 )
35X-RAY DIFFRACTION35chain 'I' and (resid 430 through 512 )
36X-RAY DIFFRACTION36chain 'I' and (resid 513 through 603 )
37X-RAY DIFFRACTION37chain 'I' and (resid 604 through 679 )
38X-RAY DIFFRACTION38chain 'I' and (resid 680 through 707 )

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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