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- PDB-4ay0: High resolution crystal structure of the monomeric subunit-free C... -

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Basic information

Entry
Database: PDB / ID: 4ay0
TitleHigh resolution crystal structure of the monomeric subunit-free Caf1M chaperone
ComponentsCHAPERONE PROTEIN CAF1M
KeywordsCHAPERONE / AMINO ACID MOTIFS / BACTERIAL CAPSULES / BACTERIAL PROTEINS / GENE EXPRESSION REGULATION / MOLECULAR CHAPERONES / PROTEIN BINDING / PROTEIN CONFORMATION
Function / homology
Function and homology information


chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chaperone protein caf1M
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAPERONE PROTEIN CAF1M
B: CHAPERONE PROTEIN CAF1M


Theoretical massNumber of molelcules
Total (without water)48,8422
Polymers48,8422
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-13 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.767, 56.767, 248.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 24420.912 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PTCA1/CAF1MD2-11, D113-129 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26926
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETIONS OF RESIDUES 2-12 AT THE N-TERMINUS AND 113-129 IN THE F1G1 LOOP.

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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: 2.43 Å3/Da / Density % sol: 49.41 % / Description: NONE
Crystal growpH: 5.5 / Details: 40% PEG 600 AND 0.1 M CITRATE, PH 5.5

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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: 1.45→62.07 Å / Num. obs: 79538 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 8.52 % / Biso Wilson estimate: 15.76 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.8
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A FROM PDB ENTRY 2OS7
Resolution: 1.52→28.765 Å / SU ML: 0.13 / σ(F): 1.83 / Phase error: 16.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 3446 5 %
Rwork0.1657 --
obs0.1668 69041 99.75 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46 Å2 / ksol: 0.35 e/Å3
Refinement stepCycle: LAST / Resolution: 1.52→28.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 0 406 3257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063085
X-RAY DIFFRACTIONf_angle_d1.1264231
X-RAY DIFFRACTIONf_dihedral_angle_d11.2991133
X-RAY DIFFRACTIONf_chiral_restr0.077474
X-RAY DIFFRACTIONf_plane_restr0.006558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.54090.22681410.18942632X-RAY DIFFRACTION99
1.5409-1.56290.18561430.17952631X-RAY DIFFRACTION99
1.5629-1.58620.22831420.18492608X-RAY DIFFRACTION99
1.5862-1.6110.21171160.17922612X-RAY DIFFRACTION99
1.611-1.63740.21151430.17872594X-RAY DIFFRACTION100
1.6374-1.66560.19991630.17672616X-RAY DIFFRACTION99
1.6656-1.69590.1971290.17382576X-RAY DIFFRACTION100
1.6959-1.72850.21761390.16842656X-RAY DIFFRACTION100
1.7285-1.76380.20061290.17612619X-RAY DIFFRACTION100
1.7638-1.80210.20791270.17322588X-RAY DIFFRACTION100
1.8021-1.84410.20771510.17182627X-RAY DIFFRACTION100
1.8441-1.89020.21341310.17152654X-RAY DIFFRACTION100
1.8902-1.94130.17891470.16582585X-RAY DIFFRACTION100
1.9413-1.99840.21161620.17282589X-RAY DIFFRACTION100
1.9984-2.06280.18711470.15282607X-RAY DIFFRACTION100
2.0628-2.13660.17511190.162667X-RAY DIFFRACTION100
2.1366-2.22210.16251440.16652612X-RAY DIFFRACTION100
2.2221-2.32320.20411350.16672626X-RAY DIFFRACTION100
2.3232-2.44560.19421370.16772639X-RAY DIFFRACTION100
2.4456-2.59870.18451450.16972638X-RAY DIFFRACTION100
2.5987-2.79920.19361200.17612641X-RAY DIFFRACTION100
2.7992-3.08060.18591570.17672608X-RAY DIFFRACTION100
3.0806-3.52570.20271290.1662660X-RAY DIFFRACTION100
3.5257-4.43940.15741210.14562647X-RAY DIFFRACTION100
4.4394-28.76970.1661290.15792663X-RAY DIFFRACTION100
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)
19.1420.3742-7.6680.5561-0.80089.3875-0.17970.0911-0.1203-0.0510.0521-0.0866-0.0225-0.00170.12530.13190.0288-0.00970.0644-0.01730.080333.722527.8714-0.8772
28.4572.5864-7.26942.7595-1.41536.8656-0.0258-0.395-0.7550.1305-0.2334-0.3258-0.030.73310.24990.11050.0329-0.02020.23460.0210.130341.809624.14965.3032
38.1821-4.2869-1.31182.28560.36412.2693-0.54910.04770.5209-0.02390.0855-0.1115-0.30090.80880.42980.1279-0.02-0.11750.45530.1040.269450.064631.457710.1301
48.1385-2.68467.00887.6505-7.19719.6489-0.6306-0.3240.34370.6330.1301-0.5537-0.92070.24830.48880.21770.0307-0.07310.16620.01040.23733.070540.10947.7228
52.06651.05071.24011.0649-0.24631.9517-0.2682-0.16340.24970.16090.08470.0261-0.28760.19320.17870.17460.0188-0.04030.1892-0.01170.123939.063131.352414.3399
68.52277.3873-4.2877.8959-1.54455.3348-0.2155-0.1809-0.90880.29780.4102-0.71710.14880.9609-0.16880.15620.0987-0.02290.478-0.00970.309652.346522.89845.5333
76.3452-3.5529-4.10993.98022.41395.1242-0.0478-0.4146-0.01530.01750.02560.0769-0.054-0.09980.00130.09780.02640.00690.0974-0.00480.096831.431527.022812.6451
85.06792.05820.99741.8037-0.76712.3478-0.0238-0.17330.2440.0653-0.02280.0764-0.1006-0.15160.03120.12110.056-0.01530.0802-0.00590.128324.139733.11335.0993
92.00151.465.8671.20831.26182.9356-0.02691.14680.16740.3769-0.2658-0.9582-0.41251.43790.23030.2067-0.043-0.12920.49950.13750.428947.899935.26168.0151
106.39851.60886.54991.42041.48556.64940.07490.84560.00090.2112-0.1351-0.3652-0.06460.73870.13210.16110.0434-0.04350.16090.03370.205138.982733.30013.2527
116.25015.8943-1.76066.3730.37887.2779-0.1903-0.2379-0.0575-0.0962-0.03890.10450.603-0.32890.25010.12850.0342-0.00830.0587-0.01930.145420.224725.88642.8591
122.0085-2.54220.19247.9724-8.72512.0145-0.08610.0071-0.83230.48460.10730.44880.4147-0.22250.03320.22030.0457-0.01090.1192-0.01890.199520.035626.2677-8.5305
130.6905-0.48950.37478.33111.6091.80960.1380.1113-0.0459-0.0976-0.12680.30680.1104-0.05340.0040.13090.0698-0.00910.1173-0.01580.109217.587242.9373-13.5462
141.7795-1.2616-0.40164.20330.79591.88030.1502-0.02880.01160.109-0.1104-0.1445-0.38540.2286-0.08890.11410.14260.01950.0686-0.02920.093520.83347.6126-11.0246
151.11180.7785-1.02881.1805-1.59153.39220.04140.0776-0.1948-0.1861-0.16-0.09570.27810.17440.11870.14030.069-0.02170.097-0.01250.115624.265336.5486-9.9441
163.7903-0.2091-0.97524.02710.05239.2035-0.07010.2856-0.1911-0.2376-0.2284-0.2288-0.10560.6840.2810.10380.0464-0.00660.1511-0.00250.103430.899144.1315-14.5454
179.0595-2.44011.79982.8618-1.13062.79350.0864-0.2094-0.05720.037-0.1345-0.1318-0.0939-0.13080.03720.13070.0599-0.00990.051-0.02020.108320.633139.3743-3.0308
183.6206-0.3720.8817.6749-4.73448.65950.03680.23330.143-0.2015-0.03560.1797-0.50340.3013-0.02850.15110.0514-0.01240.1134-0.03090.115225.23749.4659-12.6366
191.3855-1.01890.79973.2531-1.21642.18790.13820.2572-0.0781-0.0946-0.2539-0.0380.03770.20530.09830.14240.1491-0.00510.1135-0.04030.094725.705536.0881-15.8077
202.6862-2.53210.88947.1576-2.17830.9289-0.01390.0881-0.0815-0.09910.08630.13450.1126-0.375-0.0430.18750.1149-0.02870.1978-0.02930.12920.775636.2184-19.3164
217.86847.86387.68448.24678.12327.9985-0.22370.2913-0.3684-0.21520.1874-0.5186-0.13880.85190.00630.18030.0213-0.03860.2451-0.01370.144542.313525.6039-2.4944
224.90621.52743.50372.0848-0.76366.3755-0.05920.2273-0.0805-0.2644-0.08390.37990.165-0.01730.16750.17410.0721-0.04570.1123-0.04320.149534.057817.7585-16.2355
232.03367.82026.70742.02538.22646.530.42850.1635-0.26740.2957-0.1041-0.28560.1796-0.2344-0.30960.25480.0619-0.06330.1717-0.04370.211535.013226.5919-18.823
249.62572.01145.25792.00026.47318.86560.2486-0.5370.33380.6504-0.3765-0.0549-0.4380.54740.26020.4167-0.0997-0.05820.2290.01780.160347.410838.0797-10.6371
252.01173.41820.10918.38840.47724.8759-0.1245-0.72360.03990.1758-0.3112-0.2790.58170.420.40690.2884-0.0648-0.030.28340.08470.197850.417132.5938-18.6604
264.1836-0.61421.73464.32150.39619.83680.03150.5764-0.1994-0.5831-0.204-0.6772-0.09771.00740.14130.2880.02510.09990.29750.05530.302648.796514.5284-19.7146
278.868.4656-2.41169.6619-5.45926.8914-0.2578-0.2092-0.5928-0.8017-0.1524-0.50580.32640.10230.36870.19810.05460.04020.13380.00140.137843.37425.0626-24.5759
282.0097-0.1701-0.6847.08849.54782.011-0.19140.24720.7813-0.06530.10740.2719-0.20780.06860.00510.2767-0.04970.01850.1960.02360.195247.304139.8675-16.9754
296.09434.91370.80032.01152.00112.007-0.02160.10140.3099-0.71820.08170.5318-0.62790.1361-0.06170.23540.0206-0.02640.12910.00380.130938.556529.8681-20.4326
300.20950.9793-0.41284.4245-1.83850.76560.27320.14460.0471-0.55150.06050.04550.33780.0397-0.18160.4788-0.082-0.17350.2034-0.16040.115434.526610.4925-22.5077
314.45573.4881-1.03198.7584-2.4872.92420.05960.1578-0.2718-0.2309-0.2253-0.4823-0.02690.25360.17190.12220.0743-0.01630.10760.00130.104542.550215.7987-14.9701
322.00991.9976-8.33892.00631.98092.0030.5521-0.3420.51770.3456-0.8707-0.6224-0.47420.86520.4950.2882-0.1088-0.11710.41210.20730.419553.219230.0258-14.6835
332.06795.41311.4566.24911.02753.4453-0.18690.24620.2334-0.28790.03120.234-0.0222-0.16910.11780.1090.0719-0.0260.1124-0.03560.139634.412414.4833-14.3535
341.23360.77662.08670.80740.336.42280.001-0.06720.2403-0.0637-0.18970.6432-0.1091-1.14160.19140.12570.0328-0.00440.2305-0.04850.217428.39789.8552-5.0712
358.7955-5.84750.93456.2089-0.13022.2068-0.02490.0032-0.39880.26350.01620.31440.0879-0.06130.02740.15080.02360.00780.0603-0.01630.080642.8803-0.04522.2408
361.5995-0.07841.47121.2211-0.64514.0528-0.0355-0.0206-0.01470.1566-0.050.0767-0.07710.09960.08240.09550.0340.01130.0614-0.01070.066642.34518.02841.2677
371.73280.0881-0.08515.28261.24944.11780.11730.02440.06820.0243-0.16380.08850.10750.19980.0140.08760.0530.00350.0633-0.02390.070745.35175.772-4.0721
388.74770.10461.05396.66940.07376.29530.4465-0.2856-0.50560.8316-0.25890.01840.24770.7716-0.12070.2950.031-0.00940.186-0.00440.114148.91121.33211.47
392.3394-2.10791.13375.0171-2.4283.23980.0122-0.01460.16210.1652-0.07010.2652-0.1996-0.14950.02450.12010.03360.00820.0747-0.02760.119336.095814.82382.7694
407.2934-8.7593-1.15282.02620.43531.1798-0.2131-0.0131-0.8190.26910.06320.64270.6026-0.10940.0370.2857-0.01360.05280.08690.00480.274238.79780.73778.5083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 13:26)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 27:38)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 41:46)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 47:54)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 55:70)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 71:76)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 77:87)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 88:97)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 98:103)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 104:123)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 124:131)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 132:137)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 138:147)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 148:153)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 154:167)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 168:175)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 176:182)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 183:193)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 194:208)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 209:217)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 14:19)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 20:26)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 27:33)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 34:40)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 41:47)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 48:59)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 60:67)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 68:74)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 75:81)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 82:89)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 90:101)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 102:120)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 121:129)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 130:137)
35X-RAY DIFFRACTION35(CHAIN B AND RESID 138:151)
36X-RAY DIFFRACTION36(CHAIN B AND RESID 152:173)
37X-RAY DIFFRACTION37(CHAIN B AND RESID 174:187)
38X-RAY DIFFRACTION38(CHAIN B AND RESID 188:197)
39X-RAY DIFFRACTION39(CHAIN B AND RESID 198:211)
40X-RAY DIFFRACTION40(CHAIN B AND RESID 212:217)

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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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