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- PDB-4nwn: Computationally Designed Two-Component Self-Assembling Tetrahedra... -

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Basic information

Entry
Database: PDB / ID: 4nwn
TitleComputationally Designed Two-Component Self-Assembling Tetrahedral Cage T32-28
Components
  • Propanediol utilization: polyhedral bodies pduT
  • Uncharacterized protein
KeywordsPROTEIN BINDING / two-component / self-assembling / tetrahedron / designed protein cage / computational design / protein engineering / multimerization / nanomaterial / nanostructure
Function / homologyPeriplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / metal ion binding / Iron transporter / Uncharacterized protein / :
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.5 Å
AuthorsMcNamara, D.E. / King, N.P. / Bale, J.B. / Sheffler, W. / Baker, D. / Yeates, T.O.
CitationJournal: Nature / Year: 2014
Title: Accurate design of co-assembling multi-component protein nanomaterials.
Authors: King, N.P. / Bale, J.B. / Sheffler, W. / McNamara, D.E. / Gonen, S. / Gonen, T. / Yeates, T.O. / Baker, D.
History
DepositionDec 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Propanediol utilization: polyhedral bodies pduT
C: Uncharacterized protein
D: Propanediol utilization: polyhedral bodies pduT
E: Uncharacterized protein
F: Propanediol utilization: polyhedral bodies pduT
G: Uncharacterized protein
H: Propanediol utilization: polyhedral bodies pduT
I: Uncharacterized protein
J: Propanediol utilization: polyhedral bodies pduT
K: Uncharacterized protein
L: Propanediol utilization: polyhedral bodies pduT
M: Uncharacterized protein
N: Propanediol utilization: polyhedral bodies pduT
O: Uncharacterized protein
P: Propanediol utilization: polyhedral bodies pduT
Q: Uncharacterized protein
R: Propanediol utilization: polyhedral bodies pduT
S: Uncharacterized protein
T: Propanediol utilization: polyhedral bodies pduT
U: Uncharacterized protein
V: Propanediol utilization: polyhedral bodies pduT
W: Uncharacterized protein
X: Propanediol utilization: polyhedral bodies pduT


Theoretical massNumber of molelcules
Total (without water)446,92724
Polymers446,92724
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)246.010, 246.010, 290.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a protein cage with tetrahedral point group symmetry that comprises the contents of one asymmetric units.

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Components

#1: Protein
Uncharacterized protein


Mass: 19928.221 Da / Num. of mol.: 12
Mutation: R114L, S145L, N148A, N149A, T152A, V153T, E156L, S157A, E160A, R167A, V169I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / Gene: CJE1831, CJJ81176_1650, PduT, stm2054 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K8VQB8
#2: Protein
Propanediol utilization: polyhedral bodies pduT


Mass: 17315.658 Da / Num. of mol.: 12
Mutation: E71A, K73A, T75A, R82T, N114T, E116A, Y120L, K147V, D149T, K151F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: STm5 / Gene: B581_12628, cjj81176_1650 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1W1R1, UniProt: A0A0H3PA01*PLUS

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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: 5.69 Å3/Da / Density % sol: 78.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM sodium citrate tribasic dihydrate pH 5.6, 200 mM ammonium acetate, 24% (v/v) (+/-)-2-methyl-2,4-pentanediol, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.5→93.927 Å / Num. all: 60851 / Num. obs: 59814 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 183.99 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 13.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
4.5-4.627.450.9742.113217132171432197.3
4.62-4.747.510.822.513243932439431899.4
4.74-4.887.510.7012.973146531465418999.1
4.88-5.037.50.6953.043041030410405699
5.03-5.27.390.5463.752912929189394299
5.2-5.387.320.4654.362784927849380398.9
5.38-5.587.180.4474.482647626476368798.7
5.58-5.816.80.4044.812376323763349597.9
5.81-6.076.980.3575.472366323663339097.9
6.07-6.367.640.3196.392476724767324298.8
6.36-6.717.540.2388.432339023390310498.7
6.71-7.117.480.17311.232176921769291298.4
7.11-7.67.350.11216.62044820448278398.6
7.6-8.217.120.07224.361824318243256197.8
8.21-96.490.04932.81511415114232996.5
9-10.067.560.04141.381627216272215297.9
10.06-11.627.40.03448.521416514165191397.9
11.62-14.237.180.02954.681171111711163197.8
14.23-20.126.450.02754.9880798079125295.1
20.12-93.9277.070.02368.275187518773495.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model of 24-mer based on 3LZL and 3N79
Resolution: 4.5→93.927 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6573 / SU ML: 0.95 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3429 5981 10 %RANDOM
Rwork0.2971 ---
obs0.3017 59810 98.31 %-
all-60851 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 577.77 Å2 / Biso mean: 216.1558 Å2 / Biso min: 52.54 Å2
Refinement stepCycle: LAST / Resolution: 4.5→93.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20307 0 0 0 20307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320475
X-RAY DIFFRACTIONf_angle_d0.54628509
X-RAY DIFFRACTIONf_chiral_restr0.0163623
X-RAY DIFFRACTIONf_plane_restr0.0044243
X-RAY DIFFRACTIONf_dihedral_angle_d7.6054627
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
4.4992-4.55030.37851920.375817251917172595
4.5503-4.60380.41841980.3465177819761778100
4.6038-4.660.38022010.351218092010180999
4.66-4.7190.40431980.346717821980178299
4.719-4.78110.37931980.344117901988179099
4.7811-4.84650.38521990.331617831982178399
4.8465-4.91580.38491980.340917891987178999
4.9158-4.98920.40511960.351417571953175799
4.9892-5.06710.41651990.361417991998179999
5.0671-5.15020.41482050.349618412046184199
5.1502-5.2390.41241960.347617601956176099
5.239-5.33420.37012010.362718102011181099
5.3342-5.43680.4061960.350817671963176799
5.4368-5.54780.42321990.359317921991179299
5.5478-5.66840.40851990.349417891988178999
5.6684-5.80020.42491960.373217631959176397
5.8002-5.94530.42361950.373617621957176297
5.9453-6.1060.42542000.354517971997179799
6.106-6.28560.41672000.362717971997179799
6.2856-6.48850.41811990.331817891988178998
6.4885-6.72030.40822010.337718092010180999
6.7203-6.98930.32662010.316318102011181099
6.9893-7.30730.31931980.272117821980178298
7.3073-7.69240.28582020.257818162018181698
7.6924-8.17410.28982000.227418052005180598
8.1741-8.80470.24671970.202817731970177396
8.8047-9.690.23782000.202818022002180298
9.69-11.09020.24852030.21418252028182598
11.0902-13.96520.3042050.237218402045184098
13.9652-93.94780.39092090.371918882097188896
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)
16.34150.1569-1.20963.6634-0.85142.8809-0.06460.426-0.99670.31440.04691.8851-0.4704-0.26880.01981.15670.20120.20240.3181-0.60840.5144139.2699-34.075567.9931
25.58872.24541.50114.26491.1342.2968-0.24132.10170.56080.52780.65840.4757-0.05080.4494-0.05530.863-0.06870.20561.39770.27921.353157.0791-39.778744.558
33.95980.61061.18044.0311.36760.7284-0.61260.88590.19110.22591.0314-0.4671-1.61450.0498-0.02263.06580.3566-0.08560.86820.4270.5048138.8186-0.719872.2998
42.4684-1.0181-1.23974.3282-0.80455.7631-0.8234-0.2514-0.61050.78030.11990.7651-1.02880.08741.50592.3114-0.2453-0.35450.74560.25012.437128.943927.113170.5792
51.73582.7337-0.73528.94820.69961.1556-0.19510.34250.1951-2.0553-0.4092-0.77090.1109-0.39390.19921.80260.1317-0.13620.75320.17460.8162114.5921-20.003285.6558
60.98810.4631-0.11182.83380.35822.7197-0.12240.0767-0.6887-0.31070.745-0.52551.4544-0.02790.95652.4764-0.38421.44730.4080.72540.371791.479-39.334285.7493
73.3935-2.2173-0.0117.4296-4.89394.2236-0.37940.62330.6207-0.30130.0859-0.81781.4489-0.430.15691.61910.0399-0.00392.4056-0.64111.2878139.5506-46.7336-1.1239
81.4118-1.2353-0.04893.81540.90554.8014-0.47810.6053-0.29910.7270.5340.71130.66010.07410.56440.79450.1206-0.11742.0324-0.7741.521146.4331-58.139926.349
91.68880.89460.54090.46840.58110.9031-1.06450.4858-0.4675-0.4373-0.53551.1275-0.2904-1.3182-2.43331.0436-0.6575-0.66731.691-2.67942.0562121.1924-31.5467-24.8015
101.420.53460.21783.57910.31951.07660.8659-0.4271-0.036-1.6574-0.5305-1.0499-0.99521.17320.63842.0034-0.34051.05242.7701-0.10112.1515133.4044-3.6882-27.92
113.7545-0.46762.3092.33870.36592.9301-0.2042-0.82530.48481.01140.7528-1.5130.16750.9826-0.00750.65990.6783-0.28812.1104-1.55470.9173108.9303-58.2355-8.4963
123.5781.2501-2.45272.11440.57982.93920.00061.04720.9003-1.27710.71710.6006-0.4476-0.81910.72441.9140.0599-1.30541.6292-1.29223.133578.9894-57.7238-12.3681
134.1399-1.0291.15343.6013-0.62941.4246-0.42650.29040.73940.19190.48620.9549-0.4193-0.50650.46231.37940.77540.30380.87131.22382.5571111.419643.95929.3521
143.95690.43970.65652.7196-1.18412.60150.09310.73410.01631.3527-0.6931-1.81980.0170.82790.87781.6177-0.19970.49380.57950.67722.1205135.408138.82645.7915
151.62850.80960.73371.9016-0.25543.76770.3627-0.11120.0372-1.0811-1.0339-0.00090.3371-0.4178-0.29682.89410.9350.08842.25840.0610.2915117.311133.9699-2.0889
161.34320.09640.86772.70761.991.98730.63430.38221.862-2.77470.32561.24860.1423-1.0767-0.23512.72360.57130.95183.15961.39843.0163115.121517.5292-27.2079
172.3409-0.48110.73741.47350.62112.92750.39191.6762-0.8792-0.8472-0.6022-0.545-0.61071.4143-0.51071.8596-0.1175-0.1373.03350.04450.3585.349638.88198.4549
180.81441.4035-0.47553.7137-1.3050.4543-0.6370.9204-0.9333-0.3870.4570.89550.1671.86540.45781.69570.3844-0.18412.9709-0.70611.54960.390635.545124.9979
191.1698-0.66550.03311.93831.25325.269-0.38140.1549-0.4961-0.021.55020.80030.3506-1.27231.18812.4225-0.16951.55631.17940.10672.790454.495-35.768354.0393
202.8842-1.46640.40652.30971.2553.9640.7354-1.0074-0.08030.8084-0.06441.30260.08180.178-0.10551.5834-0.36541.2271.7284-0.38691.725966.6108-27.381680.1575
210.1209-0.0909-0.05190.91190.82990.754-0.4360.2467-0.1381-0.02780.14250.43330.9085-0.56920.01343.56940.4448-1.2011.738-2.01213.509148.8854-36.91521.0089
223.3886-0.3927-0.19463.3954-1.16928.2351-0.96810.7176-2.28410.1101-0.32680.5863-0.68670.14980.29981.2773-0.23430.20111.7766-0.76653.005263.922-61.706811.0418
230.6916-0.78530.67223.7961-0.99545.4743-0.6075-3.09671.72110.50721.2541-0.33790.64571.590.16311.5481-0.21960.12143.1684-1.0872.311943.9618-8.455737.7709
244.41390.4368-2.83314.1118-2.82083.9153-0.00091.71390.4916-0.71961.56030.7970.68320.5326-1.28741.71370.5286-0.67692.2453-0.8142.60844.501613.735116.9009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 183 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 158 )B0
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 184 )C0
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 158 )D0
5X-RAY DIFFRACTION5chain 'E' and (resid 2 through 184 )E0
6X-RAY DIFFRACTION6chain 'F' and (resid 2 through 158 )F0
7X-RAY DIFFRACTION7chain 'G' and (resid 2 through 184 )G0
8X-RAY DIFFRACTION8chain 'H' and (resid 2 through 158 )H0
9X-RAY DIFFRACTION9chain 'I' and (resid 2 through 183 )I0
10X-RAY DIFFRACTION10chain 'J' and (resid 2 through 158 )J0
11X-RAY DIFFRACTION11chain 'K' and (resid 2 through 184 )K0
12X-RAY DIFFRACTION12chain 'L' and (resid 2 through 158 )L0
13X-RAY DIFFRACTION13chain 'M' and (resid 2 through 182 )M0
14X-RAY DIFFRACTION14chain 'N' and (resid 2 through 158 )N0
15X-RAY DIFFRACTION15chain 'O' and (resid 2 through 183 )O0
16X-RAY DIFFRACTION16chain 'P' and (resid 2 through 158 )P0
17X-RAY DIFFRACTION17chain 'Q' and (resid 2 through 184 )Q0
18X-RAY DIFFRACTION18chain 'R' and (resid 2 through 158 )R0
19X-RAY DIFFRACTION19chain 'S' and (resid 2 through 184 )S0
20X-RAY DIFFRACTION20chain 'T' and (resid 2 through 158 )T0
21X-RAY DIFFRACTION21chain 'U' and (resid 2 through 184 )U0
22X-RAY DIFFRACTION22chain 'V' and (resid 2 through 158 )V0
23X-RAY DIFFRACTION23chain 'W' and (resid 2 through 184 )W0
24X-RAY DIFFRACTION24chain 'X' and (resid 2 through 158 )X0

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