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- PDB-5kba: Computational Design of Self-Assembling Cyclic Protein Homooligomers -

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Basic information

Entry
Database: PDB / ID: 5kba
TitleComputational Design of Self-Assembling Cyclic Protein Homooligomers
ComponentsDesigned protein ANK1C2
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.601 Å
AuthorsSankaran, B. / Zwart, P.H. / Fallas, J.A. / Pereira, J.H. / Ueda, G. / Baker, D.
CitationJournal: Nat Chem / Year: 2017
Title: Computational design of self-assembling cyclic protein homo-oligomers.
Authors: Fallas, J.A. / Ueda, G. / Sheffler, W. / Nguyen, V. / McNamara, D.E. / Sankaran, B. / Pereira, J.H. / Parmeggiani, F. / Brunette, T.J. / Cascio, D. / Yeates, T.R. / Zwart, P. / Baker, D.
History
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed protein ANK1C2
B: Designed protein ANK1C2
C: Designed protein ANK1C2
D: Designed protein ANK1C2


Theoretical massNumber of molelcules
Total (without water)72,5204
Polymers72,5204
Non-polymers00
Water1,71195
1
A: Designed protein ANK1C2
B: Designed protein ANK1C2


Theoretical massNumber of molelcules
Total (without water)36,2602
Polymers36,2602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-7 kcal/mol
Surface area13390 Å2
MethodPISA
2
C: Designed protein ANK1C2
D: Designed protein ANK1C2


Theoretical massNumber of molelcules
Total (without water)36,2602
Polymers36,2602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-8 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.372, 48.817, 139.267
Angle α, β, γ (deg.)90.00, 98.87, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 1:157 )
211chain 'B' and (resseq 1:157 )
311chain 'C' and (resseq 1:157 )
411chain 'D' and (resseq 1:157 )
DetailsDimer according to SAXS

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Components

#1: Protein
Designed protein ANK1C2


Mass: 18129.912 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.4 M Sodium Chloride, 0.1 M Tris-HCl pH 8.5 and 30 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 19299 / % possible obs: 98 % / Redundancy: 7.2 % / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 2.601→19.907 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 25.66
RfactorNum. reflection% reflection
Rfree0.2388 1017 5.36 %
Rwork0.201 --
obs0.203 18970 97.99 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 34.722 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.9893 Å20 Å2-2.7849 Å2
2--1.0965 Å2-0 Å2
3---1.8928 Å2
Refinement stepCycle: LAST / Resolution: 2.601→19.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4724 0 0 95 4819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034778
X-RAY DIFFRACTIONf_angle_d0.7386464
X-RAY DIFFRACTIONf_dihedral_angle_d14.8631766
X-RAY DIFFRACTIONf_chiral_restr0.053744
X-RAY DIFFRACTIONf_plane_restr0.004886
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1172X-RAY DIFFRACTIONPOSITIONAL
12B1172X-RAY DIFFRACTIONPOSITIONAL0.445
13C1172X-RAY DIFFRACTIONPOSITIONAL0.641
14D1172X-RAY DIFFRACTIONPOSITIONAL0.519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.73790.33391290.27992235X-RAY DIFFRACTION86
2.7379-2.90890.35511270.27222613X-RAY DIFFRACTION100
2.9089-3.13280.27341540.24932563X-RAY DIFFRACTION100
3.1328-3.44650.28271580.22022608X-RAY DIFFRACTION100
3.4465-3.94190.2091530.18222603X-RAY DIFFRACTION100
3.9419-4.95370.21031420.16762628X-RAY DIFFRACTION100
4.9537-19.90720.19451540.1752703X-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)
10.45770.2354-0.08220.3265-0.24510.22610.0094-0.09520.11850.0602-0.0689-0.0614-0.283-0.0563-0.06940.16420.03190.01310.0833-0.0530.2241-3.447321.821442.5186
20.3871-0.23810.19710.9352-0.61470.4166-0.01520.0090.47950.1306-0.2332-0.2505-0.3036-0.0853-0.07410.21440.03160.02650.11150.00130.19975.654919.725140.7961
30.0441-0.05950.03140.11020.01380.12690.0878-0.0864-0.00930.0533-0.02080.075-0.02430.01560.04090.1048-0.2051-0.038-0.00060.02310.23870.186710.112943.7086
40.1834-0.01770.20150.4794-0.27790.3581-0.03590.03010.1587-0.1112-0.1983-0.05910.02630.159-0.02410.3192-0.02290.00030.1886-0.00130.175311.905915.104537.1251
50.2554-0.1073-0.0740.09880.11210.14260.1126-0.09220.06350.01170.0152-0.1328-0.0545-0.02270.1770.1281-0.15050.0318-0.21190.11280.07611.52698.99447.0184
60.8314-0.3596-0.4970.45870.15880.7943-0.11660.0743-0.2086-0.08450.01450.11260.1416-0.2277-0.21290.1914-0.01510.02670.13740.12530.092421.56210.665539.4446
70.9541-0.22230.1910.2565-0.30490.357-0.0377-0.23440.21470.1162-0.1651-0.1402-0.28840.0713-0.02260.1363-0.18190.1145-0.06950.3365-0.138820.23156.402350.6024
80.20020.04580.0010.0099-0.0002-0.00010.01750.09090.1018-0.0244-0.1074-0.1658-0.03830.2064-0.169-0.0027-0.1190.16440.3410.21190.354129.94567.984142.7421
90.09690.0554-0.03090.1703-0.02610.0740.06-0.08890.06750.119-0.11730.0490.0246-0.0016-0.09610.188-0.3261-0.04880.42280.34980.386529.50815.971854.9117
100.2901-0.05290.11760.19140.01990.344-0.14960.02850.11270.0467-0.0718-0.0489-0.1810.1565-1.02580.2418-0.0696-0.150.3140.00770.073725.7666-14.759173.6888
110.3336-0.54220.29870.9161-0.38880.56020.1239-0.0283-0.04190.02360.10170.09760.1018-0.01720.54480.28360.09950.07980.07390.06410.040820.7241-20.654168.3047
120.0757-0.12850.05220.2084-0.08410.0358-0.02920.02310.06850.1367-0.007-0.022-0.14990.0166-0.17620.1633-0.17940.05590.18230.1621-0.141619.4046-9.870264.6258
130.2985-0.20850.3130.1496-0.19780.4863-0.09360.05410.0784-0.0317-0.0578-0.08880.09820.181-0.02470.1582-0.01670.01340.10350.01770.081515.6987-19.323559.7796
140.19550.0310.15030.26170.2180.37560.0082-0.13780.04890.1227-0.06860.0841-0.0335-0.1098-0.2956-0.0051-0.2080.16270.04220.123-0.13213.1385-8.167358.1026
150.5324-0.3998-0.2540.77510.27870.32420.0698-0.0662-0.1425-0.02990.08070.13530.13630.00540.26120.2037-0.0465-0.06210.06090.03410.17624.8029-14.295854.6059
160.53090.2338-0.15620.46560.35720.54290.12920.03840.0932-0.17720.06840.0501-0.24990.16440.35140.2301-0.0786-0.0718-0.06130.05550.12972.8252-10.381349.4747
170.2061-0.0150.18140.41740.10710.19520.0479-0.1413-0.17630.1151-0.06940.16320.0847-0.0829-0.4131-0.1288-0.3385-0.0254-0.18480.14450.1573-5.2487-5.343451.0985
180.0144-0.0041-0.0040.0050.00710.0063-0.05040.0140.1749-0.0101-0.16870.26260.12680.18410.00010.70430.02610.28880.6845-0.03480.763514.5364-7.6344-4.0926
190.00150.0029-0.00040.00650.00350.00630.05920.0118-0.08960.00210.0435-0.06770.05830.1873-0.00021.06990.16390.2870.83110.20441.20838.674-14.3459-0.0908
200.01170.00520.00790.00220.00480.00780.1493-0.1108-0.0857-0.03550.211-0.0918-0.21570.2220.00130.8072-0.00290.13751.18810.21771.075817.9934-4.10422.09
210.003-0.0052-0.00120.0119-0.00420.0092-0.0867-0.0534-0.00250.0074-0.0096-0.14-0.06980.3572-00.7407-0.12040.04670.7001-0.02030.54387.8602-0.48733.4481
220.0022-0.0034-0.0010.00340.00220.0061-0.0355-0.0528-0.0550.06440.00180.02240.07030.0590.00070.75450.29240.30440.96960.40560.90937.1958-9.71438.8498
230.0649-0.01590.0140.00790.00510.01690.0648-0.0053-0.2534-0.00590.0629-0.20370.18490.1876-0.00060.7808-0.21780.08261.196-0.11640.859515.83173.49249.7793
240.0015-0.005-0.00370.0330.03290.0304-0.1594-0.24390.0668-0.25860.04520.219-0.16080.3930.00010.6483-0.05790.19930.77350.00350.55843.82873.10210.5222
250.01180.0265-0.00860.067-0.02380.00730.0425-0.20620.2847-0.2550.0813-0.1067-0.54240.2529-0.00191.0299-0.36370.11251.2679-0.11610.981611.66588.245615.777
260.00160.0019-0.00050.11050.09140.0759-0.0121-0.4870.1698-0.2790.0548-0.0237-0.13310.1288-0.00990.8505-0.30650.40610.8142-0.16480.93430.411210.775214.4514
270.01510.0152-0.00940.0129-0.00940.01270.1840.02890.2231-0.1622-0.0239-0.069-0.0743-0.0070.00141.3195-0.33910.14461.1468-0.34261.15869.210419.022318.5756
280.00090.0009-0.00140.0118-0.00990.00760.0506-0.0720.0491-0.06230.0247-0.0433-0.12720.02750.00031.4325-0.09470.35630.8715-0.11781.41420.636722.150912.4377
290.0004-0.00190.00140.01-0.00940.00960.0460.03270.1311-0.07210.02190.0992-0.1139-0.0180.00131.57530.01550.40440.8712-0.0151.4827-5.732718.713218.6856
300.0053-0.0012-0.00730.02120.0490.11520.15190.04670.0591-0.0420.03390.14110.0296-0.03890.09111.09510.21320.21140.57160.27891.2268-28.359515.358924.9706
310.43210.11030.25670.03120.06560.15730.37830.13590.46490.05760.06990.2329-0.6836-0.02460.19520.6510.02040.14340.47490.23630.575-24.91336.937228.097
320.0767-0.0013-0.01390.00030.00010.00230.067-0.09780.1908-0.05010.01190.0887-0.0385-0.01010.00340.9744-0.17270.26240.53210.18011.0117-16.411713.651324.3167
330.0446-0.01980.02070.0309-0.0260.02460.1736-0.08770.4652-0.03320.0803-0.1968-0.67690.30250.00980.5209-0.11250.06780.43710.08660.4104-19.32422.169432.3627
340.01780.0175-0.02110.0156-0.01950.02380.18860.0138-0.1463-0.0318-0.10880.0875-0.15140.08110.00040.4484-0.03310.02490.43130.12610.4044-16.9179-1.472922.2814
350.0021-0.00280.00430.0045-0.00590.00870.064-0.00320.0826-0.10720.08970.005-0.18530.13260.00020.5177-0.12840.21950.67030.03250.5484-9.81525.550121.9409
360.1914-0.14340.09980.1084-0.07710.0577-0.4013-0.2289-0.07830.1328-0.1619-0.2268-0.30280.6852-0.01420.72250.11710.10840.77070.32960.5946-12.8489-5.21731.1611
370.02360.00390.01350.21920.02790.0158-0.2649-0.3428-0.0059-0.2644-0.02780.11980.33910.7282-0.01780.62860.14310.22510.62740.17220.5406-9.037-6.094720.0868
380.0227-0.04020.00810.0763-0.01040.0053-0.1375-0.068-0.16450.0491-0.06920.14550.08430.1028-0.1321.07210.470.36281.06560.46541.31-8.9496-14.837929.3236
390.00020.00250.00060.02160.00730.0037-0.0976-0.0537-0.01770.06930.0064-0.03110.24180.1315-0.0011.42020.270.52760.81090.12491.2856-6.9908-15.708317.0588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:24)
2X-RAY DIFFRACTION2chain 'A' and (resseq 25:48)
3X-RAY DIFFRACTION3chain 'A' and (resseq 49:57)
4X-RAY DIFFRACTION4chain 'A' and (resseq 58:71)
5X-RAY DIFFRACTION5chain 'A' and (resseq 72:91)
6X-RAY DIFFRACTION6chain 'A' and (resseq 92:104)
7X-RAY DIFFRACTION7chain 'A' and (resseq 105:124)
8X-RAY DIFFRACTION8chain 'A' and (resseq 125:137)
9X-RAY DIFFRACTION9chain 'A' and (resseq 138:157)
10X-RAY DIFFRACTION10chain 'B' and (resseq -2:24)
11X-RAY DIFFRACTION11chain 'B' and (resseq 25:38)
12X-RAY DIFFRACTION12chain 'B' and (resseq 39:57)
13X-RAY DIFFRACTION13chain 'B' and (resseq 58:71)
14X-RAY DIFFRACTION14chain 'B' and (resseq 72:91)
15X-RAY DIFFRACTION15chain 'B' and (resseq 92:114)
16X-RAY DIFFRACTION16chain 'B' and (resseq 115:137)
17X-RAY DIFFRACTION17chain 'B' and (resseq 138:157)
18X-RAY DIFFRACTION18chain 'C' and (resseq 0:13)
19X-RAY DIFFRACTION19chain 'C' and (resseq 14:24)
20X-RAY DIFFRACTION20chain 'C' and (resseq 25:38)
21X-RAY DIFFRACTION21chain 'C' and (resseq 39:48)
22X-RAY DIFFRACTION22chain 'C' and (resseq 49:58)
23X-RAY DIFFRACTION23chain 'C' and (resseq 59:71)
24X-RAY DIFFRACTION24chain 'C' and (resseq 72:89)
25X-RAY DIFFRACTION25chain 'C' and (resseq 90:104)
26X-RAY DIFFRACTION26chain 'C' and (resseq 105:124)
27X-RAY DIFFRACTION27chain 'C' and (resseq 125:137)
28X-RAY DIFFRACTION28chain 'C' and (resseq 138:147)
29X-RAY DIFFRACTION29chain 'C' and (resseq 148:157)
30X-RAY DIFFRACTION30chain 'D' and (resseq 1:24)
31X-RAY DIFFRACTION31chain 'D' and (resseq 25:48)
32X-RAY DIFFRACTION32chain 'D' and (resseq 49:57)
33X-RAY DIFFRACTION33chain 'D' and (resseq 58:71)
34X-RAY DIFFRACTION34chain 'D' and (resseq 72:81)
35X-RAY DIFFRACTION35chain 'D' and (resseq 82:90)
36X-RAY DIFFRACTION36chain 'D' and (resseq 91:104)
37X-RAY DIFFRACTION37chain 'D' and (resseq 105:124)
38X-RAY DIFFRACTION38chain 'D' and (resseq 125:137)
39X-RAY DIFFRACTION39chain 'D' and (resseq 138:157)

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