[English] 日本語
Yorodumi
- PDB-7bim: A de novo designed nonameric coiled coil, CC-Type2-(GgLaId)4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bim
TitleA de novo designed nonameric coiled coil, CC-Type2-(GgLaId)4
ComponentsNonameric de novo coiled coil CC-Type2-(GgLaId)4
KeywordsDE NOVO PROTEIN / coiled coil / alpha-helical barrel / nonamer / synthetic
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.64 Å
AuthorsShelley, K.L. / Rhys, G.G. / Dawson, W.M. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00661X/1 United Kingdom
CitationJournal: Chem Sci / Year: 2021
Title: Coiled coils 9-to-5: rational de novo design of alpha-helical barrels with tunable oligomeric states.
Authors: Dawson, W.M. / Martin, F.J.O. / Rhys, G.G. / Shelley, K.L. / Brady, R.L. / Woolfson, D.N.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / struct
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
B: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
C: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
D: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
E: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
F: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
G: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
H: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
I: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
J: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
K: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
L: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
M: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
N: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
O: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
P: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Q: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
R: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
S: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
T: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
U: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
V: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
W: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
X: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Y: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Z: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
a: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
b: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
c: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
d: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
e: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
f: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
g: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
h: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
i: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
j: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,44882
Polymers114,43636
Non-polymers4,01246
Water6,810378
1
A: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
B: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
C: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
D: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
E: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
F: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
G: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
H: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
I: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
hetero molecules


  • defined by author&software
  • Evidence: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments ...Evidence: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments indicate that that the sequence is hexameric in aqueous solution.
  • 29.6 kDa, 9 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)29,61821
Polymers28,6099
Non-polymers1,00912
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18860 Å2
ΔGint-142 kcal/mol
Surface area11570 Å2
MethodPISA
2
J: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
K: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
L: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
M: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
N: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
O: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
P: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Q: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
R: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
hetero molecules


  • defined by author&software
  • Evidence: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments ...Evidence: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments indicate that that the sequence is hexameric in aqueous solution.
  • 29.7 kDa, 9 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)29,74222
Polymers28,6099
Non-polymers1,13313
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18910 Å2
ΔGint-150 kcal/mol
Surface area11720 Å2
MethodPISA
3
S: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
T: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
U: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
V: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
W: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
X: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Y: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Z: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
a: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
hetero molecules


  • defined by author&software
  • Evidence: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments ...Evidence: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments indicate that that the sequence is hexameric in aqueous solution.
  • 29.5 kDa, 9 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)29,53019
Polymers28,6099
Non-polymers92110
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18250 Å2
ΔGint-167 kcal/mol
Surface area11920 Å2
MethodPISA
4
b: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
c: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
d: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
e: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
f: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
g: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
h: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
i: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
j: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
hetero molecules


  • defined by author&software
  • Evidence: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments ...Evidence: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments indicate that that the sequence is hexameric in aqueous solution.
  • 29.6 kDa, 9 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)29,55820
Polymers28,6099
Non-polymers94911
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18440 Å2
ΔGint-152 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.210, 128.080, 71.450
Angle α, β, γ (deg.)90.000, 110.670, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide ...
Nonameric de novo coiled coil CC-Type2-(GgLaId)4


Mass: 3178.767 Da / Num. of mol.: 36 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M ammonium acetate, 0.05 M Na HEPES, 12.5% v/v propan-2-ol. 25% v/v glycerol added to crystal as cryo-protectant prior to cryo-cooling.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: DIAMOND / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→66.85 Å / Num. obs: 146091 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.486 Å2 / CC1/2: 0.9993 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Net I/σ(I): 14.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.45-66.916.60.0294573310.9990.0120.03199
1.64-1.676.91.4291.473220.5260.5831.545100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
xia20.5.48-g3279616-dials-1.3data reduction
xia20.5.48-g3279616-dials-1.3data scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.64→66.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.079 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Repeated attempts to model solvent within the observed density in the centre of each barrel pore were inconsistent. Therefore we have included representative solvent molecules to fit the ...Details: Repeated attempts to model solvent within the observed density in the centre of each barrel pore were inconsistent. Therefore we have included representative solvent molecules to fit the density as well as possible; however we note that the fit is poor, and that these solvent molecules do not make the expected stabilising contacts with the surrounding protein.
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 7270 4.98 %RANDOM
Rwork0.1823 ---
obs0.1834 138782 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 139.17 Å2 / Biso mean: 33.214 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.42 Å2
2---1.09 Å20 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 1.64→66.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8023 0 262 378 8663
Biso mean--58.78 42.17 -
Num. residues----1107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198422
X-RAY DIFFRACTIONr_bond_other_d0.0030.028933
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.95911087
X-RAY DIFFRACTIONr_angle_other_deg1.2452.89620825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.21551077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.36225.909308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16151804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021308
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 544 -
Rwork0.292 10267 -
all-10811 -
obs--99.98 %
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)
10.7955-0.18960.09888.1914-1.09620.944-0.0111-0.04020.01930.14950.05480.3156-0.0389-0.0623-0.04370.07180.00820.02320.14540.00210.120458.03127.87923.774
20.67890.0596-0.09856.7246-0.7411.11680.02980.01620.0379-0.14310.03390.26280.001-0.1114-0.06370.04980.0171-0.00140.15590.01610.136654.76127.8816.253
31.66311.4456-0.404114.0362-1.81742.4061-0.06460.12470.084-0.75950.16520.44670.0933-0.1234-0.10060.05480.0056-0.04470.14340.02940.062257.03627.3948.351
40.99771.3007-0.17217.3916-0.56910.7057-0.06460.15740.0359-0.37840.1065-0.0360.0421-0.0537-0.0420.1439-0.0029-0.00280.16230.01950.086663.96926.6033.808
52.5252.51220.115814.56270.14041.9719-0.06290.2316-0.0178-0.58430.0463-0.4167-0.01350.05520.01650.06990.01410.03510.15270.02430.022872.14925.8674.903
61.86671.6450.069713.45030.77981.853-0.01750.1043-0.0334-0.0810.0509-0.6610.02790.1287-0.03340.01780.0070.0280.13550.01650.069277.78925.74810.819
72.15851.1762-0.274112.80410.56131.94630.0616-0.01250.03340.37020.0087-0.35180.03130.1938-0.07030.0122-0.0044-0.00640.11530.01460.063178.23625.88519.013
80.92550.0079-0.02929.26550.040.9688-0.001-0.08930.06120.42450.0486-0.06220.00810.043-0.04760.0774-0.0082-0.00130.1482-0.00250.100473.34326.78125.617
92.3016-0.90590.27213.1931-0.04642.0535-0.0203-0.17310.09560.67730.03430.2761-0.0683-0.0255-0.0140.04230.00350.02180.1205-0.00670.01865.44327.59327.525
100.78110.330.21959.38081.11980.8009-0.04430.05840.0038-0.33760.0646-0.0976-0.05540.0682-0.02030.0949-0.00890.02410.1477-0.01650.077360.89947.2739.017
110.5896-0.51830.05148.82241.1930.9606-0.00460.02110.0167-0.16950.0413-0.3307-0.03440.1032-0.03670.0740.00030.00680.1569-0.020.126465.69347.33845.661
120.7262-1.208-0.27487.18751.04010.9527-0.0311-0.0620.03950.13870.076-0.299-0.02960.0864-0.04490.07650.0125-0.02680.1627-0.01640.129565.19846.90153.905
131.1874-1.4929-0.30848.18770.65560.6788-0.0902-0.0795-0.01550.37210.0638-0.20640.01050.05340.02640.14370.0229-0.01910.1725-0.00560.091559.53246.13959.816
142.7442-1.98740.001513.3983-0.25071.4332-0.2259-0.2372-0.110.79710.21650.07590.0233-0.03150.00940.12460.03630.04270.1530.01410.020351.20645.64360.636
150.9263-0.67380.42946.1817-0.34750.7139-0.06-0.0823-0.07710.28910.09860.2432-0.0142-0.0819-0.03860.10460.01920.06010.16270.01810.138144.36945.41755.946
161.14480.05180.139314.116-0.42451.8988-0.0631-0.0609-0.09870.14750.15970.64230.0267-0.1326-0.09650.0063-0.00140.01620.12550.01870.142842.17945.27148.01
170.7146-0.0383-0.04278.2541-0.23690.7999-0.03150.0366-0.0373-0.29570.03240.28110.0114-0.0359-0.0010.0665-0.008-0.0280.1431-0.00610.133745.46145.98940.329
180.8229-0.0935-0.19268.81130.18550.7739-0.05180.0856-0.0353-0.47660.07110.1987-0.0286-0.0259-0.01920.1034-0.007-0.0180.1521-0.01060.093252.95646.60836.987
191.1620.89980.326413.78822.53733.07190.0140.1132-0.0339-0.10820.0205-0.6607-0.07190.1747-0.03450.0104-0.00740.03110.1742-0.0180.129129.5052647.858
201.45570.8992-0.247312.53132.29042.79330.0156-0.0076-0.03770.41990.1195-0.63710.0890.2026-0.1350.01680.0161-0.03480.1556-0.01710.130730.0624.77156.055
211.54160.0845-0.346814.0682.56512.387-0.0018-0.0472-0.01610.87790.0055-0.27260.16140.0772-0.00380.07890.0137-0.05090.1458-0.010.060525.25524.4762.812
221.6573-0.19150.170313.05691.71662.4429-0.0229-0.0713-0.05770.69750.0230.18590.009-0.0317-0.00010.07960.01420.020.1331-0.00710.008117.25324.57864.772
230.74090.2817-0.01829.61250.56230.8862-0.0065-0.02810.00670.22080.02510.3271-0.0108-0.061-0.01860.09480.01410.02630.1564-0.00840.10559.83525.81561.313
240.87410.3810.02956.54630.24981.04370.00560.04380.0433-0.0680.00230.2192-0.0115-0.0764-0.00790.05670.01680.01080.1613-0.00540.12576.48427.22853.931
251.13141.0550.12597.3160.3790.6942-0.06790.11760.0593-0.34520.08580.2424-0.0454-0.0408-0.01790.10080.006-0.01330.17490.00040.10698.74128.08146.002
261.26371.36030.1687.74060.70580.8075-0.0670.160.0437-0.35530.08640.0911-0.0788-0.0342-0.01940.1253-0.0050.00970.1870.00090.076215.43228.17441.436
272.06931.73130.4512.31950.74812.1857-0.06730.2007-0.0582-0.4640.1237-0.375-0.14810.1387-0.05640.0576-0.0130.04940.1889-0.00850.045523.82427.38842.051
282.4422-1.79680.082913.1896-2.01952.1379-0.0848-0.1982-0.00250.6247-0.0061-0.1691-0.135-0.01830.09080.0384-0.0175-0.00220.1675-0.00390.018728.13847.06831.272
291.0208-1.05240.23187.3235-1.72251.1692-0.0595-0.0718-0.01510.30130.07480.1169-0.0685-0.0894-0.01540.0654-0.00410.01450.17-0.00220.110421.3545.8126.753
301.4813-0.1680.121810.5768-1.85032.0612-0.00570.0352-0.01820.0350.0650.37870.0232-0.1495-0.05920.0016-0.00550.00890.1531-0.00870.076119.05644.57718.92
310.9319-0.1151-0.03037.0541-1.12251.0219-0.02830.0948-0.0312-0.22260.02430.19650.0434-0.02490.00410.0813-0.0005-0.00720.1617-0.00970.103922.52644.06511.338
320.75460.2017-0.03457.6264-1.04091.0539-0.07840.1053-0.0328-0.39490.09110.14290.07240.0111-0.01270.11080.00710.00920.1667-0.00410.0929.7344.0597.69
331.9893-0.28840.1814.4183-0.59352.0266-0.12890.2111-0.0846-0.56150.1459-0.23320.05570.1577-0.01710.05280.01270.04020.16160.00080.04737.77245.0189.549
340.9696-0.16760.29757.51970.04710.9709-0.01460.0318-0.0385-0.16680.017-0.2484-0.02330.1626-0.00240.05750.00760.03610.1670.01710.13442.55647.58416.314
351.0067-0.8295-0.05298.1852-0.41130.88730.0022-0.05160.00020.0023-0.0331-0.3453-0.03340.10130.03090.0572-0.00190.00050.17290.01850.134842.00547.3524.338
361.6455-1.97760.068511.5025-0.65721.5736-0.0843-0.16060.05950.31880.0984-0.4304-0.05190.0487-0.01410.0208-0.0192-0.01160.16830.00560.073836.36347.4430.341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 30
2X-RAY DIFFRACTION2B0 - 30
3X-RAY DIFFRACTION3C0 - 30
4X-RAY DIFFRACTION4D0 - 30
5X-RAY DIFFRACTION5E0 - 29
6X-RAY DIFFRACTION6F0 - 30
7X-RAY DIFFRACTION7G0 - 29
8X-RAY DIFFRACTION8H0 - 30
9X-RAY DIFFRACTION9I0 - 30
10X-RAY DIFFRACTION10J0 - 30
11X-RAY DIFFRACTION11K0 - 30
12X-RAY DIFFRACTION12L0 - 30
13X-RAY DIFFRACTION13M0 - 30
14X-RAY DIFFRACTION14N0 - 29
15X-RAY DIFFRACTION15O0 - 29
16X-RAY DIFFRACTION16P0 - 30
17X-RAY DIFFRACTION17Q0 - 29
18X-RAY DIFFRACTION18R0 - 30
19X-RAY DIFFRACTION19S0 - 30
20X-RAY DIFFRACTION20T0 - 30
21X-RAY DIFFRACTION21U0 - 30
22X-RAY DIFFRACTION22V0 - 29
23X-RAY DIFFRACTION23W0 - 30
24X-RAY DIFFRACTION24X0 - 30
25X-RAY DIFFRACTION25Y0 - 30
26X-RAY DIFFRACTION26Z0 - 30
27X-RAY DIFFRACTION27a0 - 30
28X-RAY DIFFRACTION28b0 - 29
29X-RAY DIFFRACTION29c0 - 30
30X-RAY DIFFRACTION30d0 - 30
31X-RAY DIFFRACTION31e0 - 30
32X-RAY DIFFRACTION32f0 - 30
33X-RAY DIFFRACTION33g0 - 30
34X-RAY DIFFRACTION34h0 - 28
35X-RAY DIFFRACTION35i0 - 30
36X-RAY DIFFRACTION36j0 - 30

+
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