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- PDB-4ayf: Crystal structure of the complex of the Caf1M:Caf1 chaperone:subu... -

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Basic information

Entry
Database: PDB / ID: 4ayf
TitleCrystal structure of the complex of the Caf1M:Caf1 chaperone:subunit preassembly complex carrying the Tyr40Ala mutation in the Caf1M chaperone
Components
  • CHAPERONE PROTEIN CAF1M
  • F1 CAPSULE ANTIGEN
KeywordsCHAPERONE/ANTIGEN / CHAPERONE-ANTIGEN COMPLEX / ANTIGENS / FIMBRIAE / MOLECULAR CHAPERONES / PROTEIN FOLDING
Function / homology
Function and homology information


capsule / pilus / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / extracellular region
Similarity search - Function
F1 capsule antigen / Caf1 Capsule antigen / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : ...F1 capsule antigen / Caf1 Capsule antigen / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chaperone protein caf1M / F1 capsule antigen
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsYu, X.D. / Dubnovitsky, A. / Pudney, A.F. / MacIntyre, S. / Knight, S.D. / Zavialov, A.V.
CitationJournal: Structure / Year: 2012
Title: Allosteric Mechanism Controls Traffic in the Chaperone/Usher Pathway.
Authors: Di Yu, X. / Dubnovitsky, A. / Pudney, A.F. / Macintyre, S. / Knight, S.D. / Zavialov, A.V.
History
DepositionJun 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHAPERONE PROTEIN CAF1M
B: F1 CAPSULE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)41,8122
Polymers41,8122
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-16.4 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.156, 68.966, 65.050
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CHAPERONE PROTEIN CAF1M / CAPSULE PROTEIN FRACTION 1


Mass: 26236.914 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-258 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PFM1-M-Y40A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26926
#2: Protein F1 CAPSULE ANTIGEN


Mass: 15575.154 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PFM1-M-Y40A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26948
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 63 TO ALA
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 35.92 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, TRIS-HCL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.07→68.97 Å / Num. obs: 18955 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.63 % / Biso Wilson estimate: 25.54 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.27
Reflection shellResolution: 2.07→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P5V

1p5v


Resolution: 2.07→47.255 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 975 5.2 %
Rwork0.1923 --
obs0.1951 18931 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 28.04 Å2
Refinement stepCycle: LAST / Resolution: 2.07→47.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 0 89 2337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072294
X-RAY DIFFRACTIONf_angle_d1.083124
X-RAY DIFFRACTIONf_dihedral_angle_d11.223782
X-RAY DIFFRACTIONf_chiral_restr0.068378
X-RAY DIFFRACTIONf_plane_restr0.005394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.17910.28751420.212527X-RAY DIFFRACTION100
2.1791-2.31570.2841480.20962550X-RAY DIFFRACTION100
2.3157-2.49440.29191590.20522549X-RAY DIFFRACTION100
2.4944-2.74540.24361410.20232554X-RAY DIFFRACTION100
2.7454-3.14260.27241180.19492578X-RAY DIFFRACTION100
3.1426-3.95910.22761240.1812602X-RAY DIFFRACTION100
3.9591-47.26730.22171430.18452596X-RAY DIFFRACTION99
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)
13.08690.42253.36662.60040.5613.98730.10540.1083-0.29350.24120.1633-0.5378-0.31840.7071-0.00880.14910.007-0.04080.30240.04850.212612.2038-5.230125.7304
22.91930.7863-0.49246.085-0.11273.4569-0.0050.04310.1468-0.2174-0.03810.5040.2003-0.1240.06570.23210.0260.03760.18920.02290.2047-3.2071-9.20887.2652
35.25050.49833.99983.3259-0.25054.83-0.05710.6652-0.0828-0.423-0.0415-0.4291-0.53631.0558-0.06810.21180.00540.05840.2972-0.01720.23739.2366-12.363318.9485
44.515-2.24492.12582.9542-1.07393.7051-0.2231-0.11920.3949-0.03220.1260.1616-0.2062-0.29-0.02090.25830.00410.03570.18380.01240.249-0.8389-10.018223.0874
56.65970.31471.02731.28410.82732.85530.4592-0.1238-0.4839-0.1055-0.3004-0.10110.61030.0527-0.06690.17960.02420.00010.13460.0310.1395.7004-17.168624.3459
62.911-1.9242.95412.2997-4.34858.63420.75340.1433-1.3916-0.0273-0.126-0.13871.5142-0.5369-0.13330.33730.0541-0.03170.209-0.09030.37093.6138-17.275616.0868
73.1735-2.82184.59965.7941-1.73318.3247-0.01870.3273-0.3533-0.02380.32120.93280.2733-1.0592-0.22160.1962-0.0652-0.00390.41950.10480.249-11.2903-9.31458.4463
80.95980.5648-1.09413.73620.09781.4255-0.10020.16690.178-0.2086-0.15310.49610.0595-0.4938-0.50580.11740.05060.02020.2463-0.06230.2157-8.0486-1.554610.2493
94.27141.77931.92510.75010.81772.989-0.2177-0.8973-0.56590.60940.393-0.08920.4096-0.5296-0.53450.35910.07640.00650.21690.07610.15793.3521-9.278328.6206
100.0616-0.04590.65220.79210.79535.2308-0.1306-0.21140.2294-0.0634-0.142-0.03510.0044-0.06550.13990.09860.0134-0.00680.1941-0.010.19816.6013-1.602432.3993
114.04650.93130.97353.56361.67132.1434-0.17260.1237-0.2001-0.52330.04030.0696-0.2978-0.53380.07110.25680.0012-0.05150.18070.01430.2075-6.732-4.54244.3405
122.71092.3143-1.92155.4304-1.33472.6821-0.23380.486-1.0932-0.77180.2602-0.92180.1867-0.1205-0.03720.4841-0.049-0.05750.2641-0.01190.3764-2.97172.6123-3.2483
134.86890.1597-0.00426.2588-0.61512.76870.26150.48590.037-0.38230.06890.2755-0.1491-0.5659-0.12070.29730.03670.03680.11550.05520.1589-5.321617.98872.6653
142.70640.1402-0.22971.9444-0.70070.26210.19380.00060.049-0.18790.10110.2717-0.5834-0.2247-0.28390.43140.0481-0.04650.15260.02480.2662-6.744510.69095.0255
152.4296-2.35590.55225.3878-0.24580.15460.4549-0.2120.29980.5149-0.01510.1286-1.31160.40420.08250.757-0.12240.0980.18630.00060.24153.659317.4418.7159
163.57420.135-0.25851.505-1.18022.17970.5416-0.0222-0.44860.3369-0.0851-0.004-0.2245-0.15310.65330.6499-0.16930.04280.1524-0.05730.26731.537315.944613.5164
173.91481.2739-2.01055.5056-2.14092.5738-0.22230.110.09710.27030.92520.9052-0.3463-0.2704-0.1580.31010.01610.01490.23510.03130.2554-8.95997.95347.2254
183.78741.7817-2.05452.884-3.09516.351-0.0346-0.3993-0.04220.4101-0.2532-0.018-0.25440.5655-2.45450.74310.0240.45650.2210.0660.2267-7.065315.955212.5654
192.37250.52330.09457.72710.92931.96660.0588-0.0990.2427-0.56150.0152-0.1526-0.61550.1597-0.10470.3711-0.08370.02590.23890.03050.25382.661316.1885.4739
200.4791-0.20630.20063.178-2.33122.3062-0.04480.01350.0062-0.76830.085-0.4410.07050.0376-0.15420.3724-0.0310.09820.21290.01170.26464.74112.80521.2451
212.6117-2.3772-1.28547.5496-0.37393.46280.23520.0344-0.0534-0.7156-0.064-0.13340.04830.21331.00990.112-0.00110.10080.3569-0.02350.293611.0546-2.987416.3697
220.95712.32592.2255.8175.58795.88750.3465-0.27140.03850.14150.6214-0.57060.3406-0.3612-0.81960.17610.0245-0.08060.28830.00710.301515.23562.600734.8118
237.9848-4.7157-5.09264.91423.08693.2512-0.0899-0.96860.4172-0.45160.61080.5085-1.00550.9438-0.28770.5945-0.1345-0.07830.40950.03980.296714.48478.694150.4345
243.8682.0334-1.37133.3643-2.85742.47340.4573-0.6045-0.08710.573-0.26060.5755-0.92870.96240.31330.52840.06340.03280.3661-0.03460.24238.432914.705248.4822
255.3459-2.7615-3.78717.09672.00698.7008-0.1642-0.0959-0.261-0.67080.0903-0.1629-0.10.3616-0.1750.1926-0.0119-0.08160.19860.01180.341112.590710.363438.8997
263.08561.3656-2.50046.9689-0.25262.2383-0.1350.66450.7827-1.6178-0.23-0.5183-0.47570.3425-0.13960.43860.06010.04010.28030.00990.285311.48084.369921.6135
275.05871.37812.41867.3464-4.48914.957-0.29990.37990.3758-1.1643-0.48010.17580.00820.04440.36060.3430.0102-0.07620.1651-0.01560.21172.29688.290322.636
286.37330.0638-3.34873.2242-0.48986.0131-0.15460.5467-0.1468-0.0782-0.18820.2553-0.0109-0.40610.37130.1283-0.0176-0.01260.1489-0.02350.21-1.16782.42835.5481
292.02031.7635-1.31554.7691-1.07813.85520.01590.00240.5597-0.0085-0.22760.8476-0.4383-0.4562-0.20070.218-0.0076-0.07180.1589-0.01830.2623-2.32929.67637.6482
301.66433.0066-2.22625.8276-4.23973.9722-0.0293-0.3464-0.08370.0028-0.4031-0.45080.930.17260.33650.2511-0.004-0.01520.20980.04520.172.92590.719446.7858
311.56190.7224-1.85064.0179-2.73983.159-0.5932-0.4166-0.5310.62050.1195-0.82030.9164-0.548-0.02060.54050.00940.1040.2273-0.00410.3371-0.08640.7553.2506
324.74993.0038-3.27689.7391-5.09559.14120.0975-0.33020.16731.004-0.1065-0.0377-1.3697-0.2817-0.04320.16910.017-0.0260.1473-0.01350.22374.18439.952840.9409
333.42962.4055-2.00693.1833-2.65682.34160.2137-0.00411.3743-0.7140.49410.5114-0.21070.133-0.11170.238-0.02380.03560.30710.09320.29538.985817.357829.2885
343.80940.2033-1.91383.9691.00073.0568-0.13390.34830.3769-0.70010.24640.2738-0.0654-0.34710.1390.17110.0052-0.1070.1066-0.01080.2099-0.55639.089230.2815
353.533.3566-0.44733.6762-0.19232.11250.68210.43020.9808-0.8331-0.55220.3424-0.8641-0.42110.01210.52170.07060.07640.3749-0.01420.3795-0.892614.721628.9616
362.2584-2.4471-1.07737.2924-3.85856.038-0.41590.00150.4953-0.5561-0.1973-0.29650.39650.5668-0.22850.3617-0.09410.05010.1798-0.0540.261211.222211.130320.7073
373.66910.3057-0.16094.80610.00752.46140.58030.47050.37880.1154-0.026-0.2565-0.30720.9441-0.48210.1944-0.031-0.00590.3367-0.01710.238511.207411.224333.652
386.3664-1.33224.22849.1466-3.31769.9410.8423-1.14340.30051.23740.20620.827-0.8328-1.3077-0.74280.4231-0.05650.04950.3256-0.00840.28812.10311.37249.2687
394.471-0.55610.48034.6772-0.19251.7579-0.0441-0.3524-0.15410.85570.2918-0.5068-0.0278-0.212-0.15110.3009-0.0076-0.06240.20520.03650.23876.18360.637148.0632
401.97940.50450.57251.51931.64265.64160.03220.1850.1292-0.13440.0475-0.0113-0.2788-0.2326-0.13850.12620.00120.02790.18680.02340.21122.88011.232424.3007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 9:17)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 18:30)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 31:38)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 39:62)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 63:74)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 75:79)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 80:89)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 90:97)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 98:104)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 125:138)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 139:146)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 147:154)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 155:163)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 164:178)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 179:185)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 186:192)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 193:198)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 199:203)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 204:221)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 222:233)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 14:20)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 21:26)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 27:32)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 33:39)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 40:46)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 47:54)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 55:61)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 62:67)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 68:72)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 73:77)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 78:83)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 84:88)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 89:98)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 99:104)
35X-RAY DIFFRACTION35(CHAIN B AND RESID 105:111)
36X-RAY DIFFRACTION36(CHAIN B AND RESID 112:119)
37X-RAY DIFFRACTION37(CHAIN B AND RESID 120:124)
38X-RAY DIFFRACTION38(CHAIN B AND RESID 125:133)
39X-RAY DIFFRACTION39(CHAIN B AND RESID 134:141)
40X-RAY DIFFRACTION40(CHAIN B AND RESID 142:149)

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Yorodumi

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  • 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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