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- PDB-4az8: Crystal structure of the complex of the Caf1M:Caf1 chaperone:subu... -

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Basic information

Entry
Database: PDB / ID: 4az8
TitleCrystal structure of the complex of the Caf1M:Caf1 chaperone:subunit preassembly complex carrying the KDKDTN insertion at the F1G1 loop region
Components
  • CHAPERONE PROTEIN CAF1M
  • F1 CAPSULE ANTIGEN
KeywordsCHAPERONE/IMMUNE SYSTEM / CHAPERONE-IMMUNE SYSTEM COMPLEX / ANTIGENS / FIMBRIAE / MOLECULAR CHAPERONES
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: 2.65 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 24, 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)42,4792
Polymers42,4792
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-15.9 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.510, 69.308, 66.035
Angle α, β, γ (deg.)90.00, 94.82, 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: 26903.574 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PFM1-M-INSA114-KDKDTN / 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PFM1-M-INSA114-KDKDTN / 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.: 42 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.76 % / 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: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 10, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.65→47.72 Å / Num. obs: 9383 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 21.68 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.3
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.37 / 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: 2.65→29.722 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 446 4.8 %
Rwork0.2212 --
obs0.2227 9352 99.88 %
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: 32.58 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 0 42 2403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062414
X-RAY DIFFRACTIONf_angle_d1.4413276
X-RAY DIFFRACTIONf_dihedral_angle_d14.917860
X-RAY DIFFRACTIONf_chiral_restr0.112380
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-3.03320.34281480.26132936X-RAY DIFFRACTION100
3.0332-3.82020.23441550.22292958X-RAY DIFFRACTION100
3.8202-29.72370.21811430.23012X-RAY DIFFRACTION100
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)
11.59731.1691.85050.40880.70182.06230.02010.2129-0.36870.1243-0.0948-0.19020.71421.15270.09470.25140.065-0.04070.2732-0.01810.447212.2396-5.103126.5936
21.61741.3717-0.73537.6057-0.44052.2732-0.3430.2264-0.1173-0.42290.6113-0.1729-0.0978-0.0022-0.22960.25150.02420.08440.29110.01080.2723-2.8516-8.90257.3151
33.221-0.37531.08230.88090.16892.62380.03011.3671-0.35810.04250.4282-0.52090.1044-0.1507-0.24370.18740.3070.01480.1747-0.03770.23816.9783-13.315216.8304
40.65540.2163-0.79680.81760.2431.1410.1701-0.15020.0407-0.3991-0.1038-0.16820.55290.09550.03850.220.08770.05330.310.02170.19886.6996-12.062728.3762
56.634-3.74862.87828.2081-7.15736.24940.1106-0.7643-0.38410.71030.35371.3352-0.0426-0.7799-0.46870.50480.05760.06980.27760.04580.3248-8.4018-7.038118.1892
64.7703-0.90840.32912.00040.3011.4095-0.46520.5173-0.6620.33190.4477-0.0597-0.3225-0.17250.01430.1715-0.00180.03970.17210.03570.34135.3357-17.288824.3325
73.4642-1.72431.51893.6444-0.84664.71480.52370.8429-0.41010.724-0.03390.61520.82630.3877-0.24870.23240.0399-0.07550.18820.01660.4274-1.1116-15.347514.017
88.10912.2446-3.11682.01250.67838.19370.77360.96820.83410.2745-0.82850.1866-0.5468-1.38230.14120.32270.0262-0.00180.39050.02890.4742-13.2813-2.48043.5769
92.60180.19851.61920.8880.14732.41970.4041-0.2547-0.2607-0.19040.07930.11941.1514-0.465-0.19820.25920.01990.01970.2332-0.00570.23910.6393-5.653425.3036
102.2293-0.8834-0.50353.42180.43930.1187-0.3914-0.87930.56460.46110.4411-0.1885-0.28290.5879-0.31740.27820.05630.04460.4661-0.02740.29688.5688-1.705238.5952
113.2622-0.14960.330.72210.26551.0991-0.12150.4848-0.3664-0.34510.0472-0.2314-0.1947-0.10950.06150.356-0.0848-0.00230.27520.00480.2109-4.1538-3.57846.3592
123.44620.18821.85981.32530.69393.16360.06290.3482-0.4523-0.8450.3537-0.2639-0.54540.1306-0.26620.4769-0.0027-0.08860.3919-0.07250.2701-0.8497.2899-3.547
139.578-0.64452.64289.1853-0.8587.1378-0.21040.29180.6567-0.18770.2281-0.3446-0.0606-0.43410.10450.26990.0145-0.00110.27860.06340.2653-5.741616.99611.6869
141.9823-1.0116-0.32666.1902-0.6953.15971.44060.5809-0.25170.1652-0.56070.86580.327-0.3605-0.74990.54840.05140.02420.27670.01630.5797-8.406620.61348.5095
151.23240.6539-0.21111.2846-0.56920.4011-0.6248-0.41740.4215-0.50760.37240.46660.0001-0.03180.30560.41960.0102-0.09610.40430.03490.2358-3.96686.86014.5894
166.34991.8815-2.91082.1345-2.75085.8079-0.5104-1.18510.1549-0.30030.07680.9856-1.30040.7250.51410.8039-0.04440.00620.2847-0.00860.42153.890621.877910.3125
175.59471.2494-1.31628.7801-0.02193.95940.9940.6833-0.18830.7670.09110.3481-0.7801-0.5196-0.73050.3852-0.03620.03030.22170.02450.2951-5.76439.995310.0521
185.8443-3.26210.35383.3990.06322.6004-0.7503-1.4171-0.28340.47890.9032-0.6061-0.03-0.9426-0.01560.58060.02720.09960.2828-0.03540.2927-6.081417.941513.026
191.59161.57920.09986.00213.3834.7636-0.07690.09850.147-0.30180.5704-0.5696-0.47790.2311-0.51280.3747-0.01770.03270.3577-0.01250.16822.403421.37834.7888
202.42370.69650.03674.0838-2.03431.483-0.24620.3260.0053-0.41830.0334-0.398-0.58780.44360.18610.4029-0.0971-0.01040.27480.0140.24.280110.13142.1906
211.3126-0.2402-0.01861.23920.50164.3153-0.19820.8669-0.6457-0.54240.1807-0.5437-1.11041.35760.00640.3723-0.176-0.02930.5272-0.0480.448911.4469-2.771817.15
220.01040.15470.2870.49561.22732.84680.474-0.36260.7276-0.66630.11180.2696-0.13260.2462-0.1040.17190.06330.0270.3156-0.11870.261715.01352.940835.3982
236.1565-1.5286-5.41853.01220.00156.94330.0012-1.33820.65120.02780.86560.6066-0.15830.5702-0.50270.79250.1039-0.070.38950.10670.169210.585610.872351.3618
241.7116-1.6879-2.2852.64043.69235.5391-0.07220.0543-0.1843-0.1087-0.25220.37140.2602-0.42750.43160.2417-0.0385-0.04710.22680.05360.283311.113611.338540.4639
252.1248-3.58491.10426.4257-2.20511.24490.90280.6520.0133-2.0529-0.225-0.7843-0.21470.6784-0.31350.35670.0870.02550.4696-0.0890.180510.05235.287521.8091
261.87-0.33860.79210.0611-0.0881.3749-0.04810.00550.40030.2641-0.2275-0.06-0.3023-0.34940.33630.29470.0538-0.07160.1782-0.08330.43331.24046.871126.2021
270.0613-0.07410.1677-0.01270.04810.9645-0.6649-0.3514-0.6512-0.3927-0.64580.7879-0.0774-0.25830.3169-0.1511-0.3235-0.23850.1903-0.21840.1781-4.31653.759637.7122
281.9901-0.3613-0.96872.47880.61040.55240.46510.01470.22630.5927-1.1968-0.0798-0.28510.57890.59650.2113-0.0104-0.07020.3282-0.01980.18860.06536.659641.0473
293.2154-2.77732.40742.9382-1.0816.6525-0.21270.0773-1.3474-0.90621.6691-0.07980.5054-1.0195-0.60680.488-0.2222-0.00470.32470.0380.379-0.0051-1.88553.7822
301.60990.7539-0.29093.6335-3.21644.56090.28420.2106-0.28360.68660.0336-0.3966-0.8447-0.5763-0.05950.13960.05770.04130.3364-0.12990.24811.19596.357847.5116
314.20152.10720.15662.39280.40555.13360.26060.3259-0.1671-0.3044-0.06360.7796-1.01310.78410.24950.37-0.0384-0.07950.19430.05650.34287.875815.277331.5341
320.201-0.1669-0.28580.09160.17040.38831.4206-0.61541.1067-0.34520.5030.1277-0.41360.354-0.03160.56280.05520.12080.35930.09290.63548.614520.605826.6924
337.42723.1974-1.71853.8899-1.10721.9379-0.10360.6150.7384-0.75630.18280.3747-0.0759-0.0482-0.05570.40510.1432-0.07130.2454-0.00370.2029-1.08858.921530.5658
342.3201-1.7244-1.66113.45171.28774.19820.2732-0.3137-0.3388-0.6976-0.47370.3421-0.7017-0.37770.14120.29050.0853-0.01430.33950.02690.40121.832414.951225.6611
354.9938-0.99580.1994.32850.43156.209-0.57570.2397-0.13920.1541-0.27570.4742-0.05270.52430.92750.26570.0023-0.00920.28170.10460.488412.83029.468225.0299
364.29690.3736-0.44332.06620.50212.10220.067-0.15470.6390.28440.30.53840.1841-0.1309-0.29030.34810.00930.08850.11850.01330.42424.137511.67345.3679
374.0030.64114.79463.96380.4081.9991-0.9275-0.43330.318-0.1964-0.3209-0.54780.1304-0.58730.7780.3048-0.1218-0.04720.29790.10450.42485.54031.621850.3689
381.2676-0.3789-0.25070.25410.27550.24440.6708-0.1159-0.4760.8545-0.2283-0.0249-0.47120.0252-0.0941-0.08940.1754-0.00370.25740.04810.23222.48670.284826.9748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 9:17)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 18:28)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 29:37)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 38:47)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 48:61)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 62:74)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 75:87)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 88:93)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 94:126)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 127:134)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 135:151)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 152:156)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 157:161)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 162:170)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 171:181)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 182:188)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 189:198)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 199:205)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 206:217)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 218:233)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 15:20)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 21:26)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 27:38)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 39:46)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 47:56)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 57:62)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 63:69)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 70:75)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 76:81)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 82:86)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 87:92)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 93:98)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 99:104)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 105:115)
35X-RAY DIFFRACTION35(CHAIN B AND RESID 116:121)
36X-RAY DIFFRACTION36(CHAIN B AND RESID 122:132)
37X-RAY DIFFRACTION37(CHAIN B AND RESID 133:140)
38X-RAY DIFFRACTION38(CHAIN B AND RESID 141:148)

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