[English] 日本語
Yorodumi
- PDB-4x2c: Clostridium difficile Fic protein_0569 mutant S31A, E35A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x2c
TitleClostridium difficile Fic protein_0569 mutant S31A, E35A
ComponentsFic family protein putative filamentation induced by cAMP protein
KeywordsSTRUCTURAL PROTEIN / Fic protein / a-helical / SE/AA mutant
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
Fido domain-containing protein / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Fic family protein putative filamentation induced by cAMP protein
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsJorgensen, R. / Dedic, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research11-104831/FSS Denmark
CitationJournal: To Be Published
Title: Structure of Clostridium difficile Fic_0569 S31A, E35A mutant at 1.8 Angstroms resolution
Authors: Jorgensen, R. / Dedic, E. / Alsarraf, H. / Welner, D. / Leeuwen, H.C. / Oestergaard, O.
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fic family protein putative filamentation induced by cAMP protein
B: Fic family protein putative filamentation induced by cAMP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3869
Polymers54,5922
Non-polymers7947
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-10 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.370, 67.290, 139.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Fic family protein putative filamentation induced by cAMP protein


Mass: 27296.156 Da / Num. of mol.: 2 / Mutation: S31A, E35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Strain: R20291 / Gene: CDR20291_0569
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C9YJ22
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M MgCl2-6xH2O 25.0 % (w/v) PEG 3350, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 11, 2014
Details: Multilayer mirror, curved to focus in the vertical (R = 400 m)
RadiationMonochromator: Bent Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03841 Å / Relative weight: 1
ReflectionResolution: 1.8→19.12 Å / Num. obs: 46011 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 26.25 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.077 / Χ2: 0.911 / Net I/σ(I): 19.04 / Num. measured all: 301559
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.90.7790.8812.343614685666630.95797.2
1.9-20.8950.5164.0836420557154830.5698.4
2-2.20.960.2857.354717835182400.3198.7
2.2-2.50.990.13714.5753202811480420.14999.1
2.5-2.80.9960.0822.2732842498549610.08799.5
2.8-30.9980.05827.4615220231923120.06399.7
3-40.9990.03840.2238452592759100.04199.7
4-50.9990.02756.9113579214021370.0399.9
5-60.9990.02754.3259869639620.02999.9
6-100.9990.02458.026335108210610.02798.1
100.9990.02258.2811923422400.02470.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.12 Å
Translation2.5 Å19.12 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
PHASER2.3.0phasing
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cuc
Resolution: 1.8→19.1 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 1378 3 %Random selection
Rwork0.1812 44575 --
obs0.1823 45953 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.91 Å2 / Biso mean: 37.758 Å2 / Biso min: 12.24 Å2
Refinement stepCycle: final / Resolution: 1.8→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 50 216 3661
Biso mean--62.29 40.66 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083598
X-RAY DIFFRACTIONf_angle_d0.9994877
X-RAY DIFFRACTIONf_chiral_restr0.04544
X-RAY DIFFRACTIONf_plane_restr0.005612
X-RAY DIFFRACTIONf_dihedral_angle_d13.1241335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8004-1.86470.36181330.29664306443997
1.8647-1.93930.27911360.24384364450098
1.9393-2.02740.26551350.22434388452399
2.0274-2.13420.26971370.19274414455199
2.1342-2.26770.22351370.17754418455599
2.2677-2.44250.21531360.16844454459099
2.4425-2.68770.18711390.16914473461299
2.6877-3.07520.20231390.166745094648100
3.0752-3.86910.19121420.161445564698100
3.8691-19.10060.21661440.18344693483799
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)
13.47623.6259-5.32544.0792-5.72198.27320.1030.8875-0.4461-0.6273-0.1354-0.71840.79690.41150.04310.460.1073-0.01870.4267-0.03820.370945.048649.246137.0752
24.1064-1.6379-1.00363.18753.20595.06350.14760.26390.1056-0.2451-0.0093-0.1666-0.14740.0159-0.11590.1922-0.0314-0.02720.21450.0420.250142.273558.872941.6549
31.56562.0457-1.78965.1360.47116.440.04250.07030.16790.1084-0.05870.3406-0.1795-0.38590.01460.13460.0087-0.02220.22330.01880.235838.351966.813751.5483
40.7444-1.0567-0.9173.79184.48577.15940.13440.06180.3268-0.60530.0979-0.1674-0.2218-0.0757-0.19390.1574-0.01190.00280.2786-0.01720.295145.695972.971347.2163
52.1121-0.49490.05187.57144.84234.91710.1558-0.06450.07080.34330.0556-0.6870.1810.2393-0.25830.2011-0.021-0.05170.25660.05270.246748.975361.235252.6569
63.3132-4.7484-0.74066.92441.68423.39740.50150.176-1.0785-0.17740.1565-0.44261.65930.2938-0.54920.54710.0397-0.11790.31550.06040.656250.118341.880754.1669
72.26241.86950.03822.2916-1.212.12130.023-0.3668-0.68280.8824-0.3379-0.53460.38010.45390.46380.40170.0404-0.08790.34710.06460.45852.612348.854961.1584
83.30613.2725-0.30463.3569-0.2072.08270.126-0.58220.59650.73320.032-0.8890.06530.6224-0.14990.3050.0148-0.05550.36490.03770.423253.16262.195860.8197
96.35441.834-1.87552.46032.25064.59590.2334-0.9112-0.43670.66760.62740.27941.2157-0.6767-1.09510.7589-0.0318-0.10260.80460.21880.923746.988647.253476.4177
107.92254.12122.62094.48525.86179.49150.2616-0.9875-1.21750.78490.37-0.03290.86970.2087-0.46810.4964-0.0303-0.14480.3860.16780.489144.111839.787566.5842
114.4641-3.1010.23492.6295-1.01631.5580.12090.0178-0.46530.15830.0530.49160.3694-0.4571-0.19570.5282-0.167-0.13850.34960.07820.539838.183436.708256.3017
123.6577-0.34150.09442.8659-0.83764.31220.078-0.2535-0.3640.31530.03560.08930.3579-0.3681-0.10460.4332-0.1095-0.04830.30130.08780.247538.084747.318764.4444
133.127-3.71193.80935.2811-2.75788.374-0.4869-0.5120.68620.9598-0.3854-0.3234-0.95190.3780.78280.4839-0.0795-0.08460.31850.01410.314845.135357.410264.8093
142.5502-0.9312-1.24248.24094.37498.52990.10390.0144-0.25140.5113-0.00190.03550.9491-0.3668-0.11570.2932-0.0425-0.06930.19580.03350.24241.197947.980652.6489
151.3225-1.22450.85847.98466.26948.3530.0403-0.02960.13830.6431-0.02650.45330.0241-0.56950.02480.3256-0.09530.09480.32410.05520.304630.950256.214951.9944
168.4292-4.3121-1.01424.3578-2.36316.95310.5066-0.71511.23851.2742-0.57070.666-0.4031-0.37490.01310.4022-0.16410.1280.4699-0.10290.498128.946456.864762.176
175.75930.8327-1.56014.5057-1.07470.59190.0031-1.102-0.69840.43920.25120.35920.7128-0.9191-0.25440.5544-0.25540.01890.71830.13890.417227.732145.988364.41
189.7865-4.1924-4.50312.13182.02372.0974-0.02660.37-0.30310.0957-0.04820.38090.9934-1.5238-0.09510.3436-0.20690.00670.44420.01010.336526.967650.808351.0504
198.8568-4.32450.97763.80461.14425.00320.1990.2161-0.04830.1277-0.25740.35490.815-0.84430.09630.2948-0.101-0.03630.3194-0.02050.181132.230551.896539.8558
204.0485-4.558-1.86346.26713.29875.19580.0489-0.1118-0.48810.0438-0.26340.23270.2476-0.82880.13780.2403-0.0556-0.07040.31460.01260.246835.177250.729831.6214
219.742-2.34432.07493.6211-3.66183.7139-1.0727-1.18460.14431.09190.39090.03250.41580.51130.53881.0867-0.16360.03850.6983-0.07680.322768.252194.095870.5797
226.80351.6507-5.06696.4663-0.67337.34680.4779-0.9785-0.17420.8439-0.18790.32090.33320.1001-0.1161.1948-0.05080.38771.17470.54161.001660.94488.141472.8246
234.2307-2.09874.26191.6109-1.47397.70110.2128-0.6650.27890.9962-0.07160.7031-0.7513-0.4448-0.1690.5542-0.13620.17750.3478-0.02810.35959.064590.469661.0786
247.72557.7961-0.45058.87020.90599.45970.12190.29960.1344-0.19520.06690.3603-0.0633-0.2326-0.22440.1855-0.0037-0.00040.17140.0160.224758.616485.641647.6265
254.20380.0975-1.34488.9576-1.63698.52620.7531-0.17791.33270.4902-0.29570.7713-1.17130.122-0.31730.3088-0.04180.11210.2453-0.04710.450850.437586.535355.2067
265.89483.21272.03459.14071.36432.1070.3415-0.36610.57950.4451-0.22330.2535-0.46730.2433-0.17840.2506-0.01910.04880.2564-0.03810.292348.824880.638857.3142
276.51712.27512.95853.37030.53383.61960.312-0.3838-0.43460.611-0.2153-0.0786-0.1394-0.0073-0.10690.2617-0.06220.00210.22030.06710.229360.200978.638855.8301
283.7917-0.5672-0.23373.14474.2965.9510.2437-0.8225-0.62041.4989-0.0593-0.65670.81180.2534-0.17850.6222-0.1737-0.14230.61230.03680.370575.190384.203866.1736
298.5497-0.25750.5795.42291.86023.53320.75620.0853-1.05090.7739-0.4075-0.85480.46710.417-0.43450.3733-0.0805-0.20790.51960.150.523679.982478.540158.2227
307.6186-0.92590.83341.6478-0.26095.2380.43170.0871-1.31230.5117-0.3446-0.4620.33320.2707-0.02940.2713-0.0149-0.10850.21820.07950.419867.700173.113353.4475
314.59254.79974.00767.00263.48013.78250.1780.7297-0.27330.15-0.205-0.82660.64311.23980.04870.25360.0743-0.04260.42130.07450.483985.398677.437746.8386
323.670.20130.71630.5025-0.07780.69560.0106-0.29810.05150.27330.0208-0.4261-0.50250.5657-0.0740.2007-0.3689-0.33430.58270.13960.427186.829589.14254.8258
334.9325-1.06320.44350.3791-0.24052.93250.1987-0.09960.14290.2722-0.2991-0.4215-0.50230.53840.00820.2425-0.1142-0.04460.28690.06570.220778.748889.15947.9697
344.2175-3.5069-2.99963.36791.87963.02730.14790.2433-1.3064-0.2732-0.46090.81920.4287-0.69510.25050.2282-0.0386-0.05360.2883-0.01170.414970.976376.623845.6494
354.94590.07282.96634.17492.03819.10210.4289-0.3055-0.21180.4549-0.1616-0.242-0.46960.0694-0.27230.2541-0.0889-0.00240.24630.05420.209970.718887.251954.5044
365.8512-0.15534.31544.16172.03335.1719-0.0887-0.46890.4720.3146-0.15580.2499-0.97220.01860.37360.391-0.1860.02180.32330.00750.161568.535895.629655.3304
376.7463-0.1171-1.43113.7426-0.26333.24350.27860.31070.305-0.0192-0.2464-0.1097-0.64830.2833-0.02470.33-0.05250.00540.23560.05560.173372.869495.610141.6237
387.5958-0.0556-3.16934.79542.29742.81831.0839-0.43190.56370.409-0.3529-0.0073-1.61220.3109-0.7090.6259-0.12790.08590.2685-0.02550.340468.0671101.456252.5421
390.7072-0.20760.06621.36451.09641.10270.0044-0.16190.28740.33210.3697-0.411-0.09280.3980.00651.179-0.19350.18570.2288-0.34330.318363.9259100.981661.9034
404.4849-4.76-2.53435.05522.5396.5089-0.1672-0.47720.33260.2914-0.21480.14970.0711-0.5240.42721.3579-0.26860.32120.4738-0.20960.552162.6845102.335868.5406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:14)A4 - 14
2X-RAY DIFFRACTION2(chain A and resid 15:28)A15 - 28
3X-RAY DIFFRACTION3(chain A and resid 29:45)A29 - 45
4X-RAY DIFFRACTION4(chain A and resid 46:56)A46 - 56
5X-RAY DIFFRACTION5(chain A and resid 57:79)A57 - 79
6X-RAY DIFFRACTION6(chain A and resid 80:84)A80 - 84
7X-RAY DIFFRACTION7(chain A and resid 85:91)A85 - 91
8X-RAY DIFFRACTION8(chain A and resid 92:100)A92 - 100
9X-RAY DIFFRACTION9(chain A and resid 126:131)A126 - 131
10X-RAY DIFFRACTION10(chain A and resid 132:140)A132 - 140
11X-RAY DIFFRACTION11(chain A and resid 141:150)A141 - 150
12X-RAY DIFFRACTION12(chain A and resid 151:164)A151 - 164
13X-RAY DIFFRACTION13(chain A and resid 165:171)A165 - 171
14X-RAY DIFFRACTION14(chain A and resid 172:185)A172 - 185
15X-RAY DIFFRACTION15(chain A and resid 186:196)A186 - 196
16X-RAY DIFFRACTION16(chain A and resid 197:204)A197 - 204
17X-RAY DIFFRACTION17(chain A and resid 205:215)A205 - 215
18X-RAY DIFFRACTION18(chain A and resid 216:223)A216 - 223
19X-RAY DIFFRACTION19(chain A and resid 224:228)A224 - 228
20X-RAY DIFFRACTION20(chain A and resid 229:235)A229 - 235
21X-RAY DIFFRACTION21(chain B and resid 4:10)B4 - 10
22X-RAY DIFFRACTION22(chain B and resid 11:15)B11 - 15
23X-RAY DIFFRACTION23(chain B and resid 16:30)B16 - 30
24X-RAY DIFFRACTION24(chain B and resid 31:38)B31 - 38
25X-RAY DIFFRACTION25(chain B and resid 39:46)B39 - 46
26X-RAY DIFFRACTION26(chain B and resid 47:56)B47 - 56
27X-RAY DIFFRACTION27(chain B and resid 57:76)B57 - 76
28X-RAY DIFFRACTION28(chain B and resid 77:81)B77 - 81
29X-RAY DIFFRACTION29(chain B and resid 82:87)B82 - 87
30X-RAY DIFFRACTION30(chain B and resid 88:100)B88 - 100
31X-RAY DIFFRACTION31(chain B and resid 129:135)B129 - 135
32X-RAY DIFFRACTION32(chain B and resid 136:146)B136 - 146
33X-RAY DIFFRACTION33(chain B and resid 147:164)B147 - 164
34X-RAY DIFFRACTION34(chain B and resid 165:169)B165 - 169
35X-RAY DIFFRACTION35(chain B and resid 170:182)B170 - 182
36X-RAY DIFFRACTION36(chain B and resid 183:194)B183 - 194
37X-RAY DIFFRACTION37(chain B and resid 195:217)B195 - 217
38X-RAY DIFFRACTION38(chain B and resid 218:223)B218 - 223
39X-RAY DIFFRACTION39(chain B and resid 224:228)B224 - 228
40X-RAY DIFFRACTION40(chain B and resid 229:233)B229 - 233

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
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

Read more