[English] 日本語
Yorodumi
- PDB-6txk: Crystal structure of thermotoga maritima E65K Ferritin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6txk
TitleCrystal structure of thermotoga maritima E65K Ferritin
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Metal binding / engineered protein
Function / homology
Function and homology information


bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / EICOSANE / Ferritin
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.359 Å
AuthorsWilk, P. / Grudnik, P. / Kumar, M. / Heddle, J. / Chakraborti, S.
Funding support Poland, 1items
OrganizationGrant numberCountry
Foundation for Polish ScienceHoming/2017-3/22 Poland
CitationJournal: Nanoscale / Year: 2021
Title: A single residue can modulate nanocage assembly in salt dependent ferritin.
Authors: Kumar, M. / Markiewicz-Mizera, J. / Janna Olmos, J.D. / Wilk, P. / Grudnik, P. / Biela, A.P. / Jemiola-Rzeminska, M. / Gorecki, A. / Chakraborti, S. / Heddle, J.G.
History
DepositionJan 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _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.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,97164
Polymers155,2158
Non-polymers5,75656
Water7,963442
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,914192
Polymers465,64624
Non-polymers17,268168
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area93910 Å2
ΔGint-597 kcal/mol
Surface area147320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.811, 175.811, 354.136
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 6 or resid 8...
21(chain B and (resid 2 through 6 or resid 8...
31(chain C and (resid 2 through 6 or resid 8...
41(chain D and (resid 2 through 6 or resid 8...
51(chain E and (resid 2 through 6 or resid 8...
61(chain F and (resid 2 through 6 or resid 8...
71(chain G and (resid 2 through 6 or resid 8...
81(chain H and (resid 2 through 6 or resid 8...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 6 or resid 8...A2 - 6
121(chain A and (resid 2 through 6 or resid 8...A8 - 9
131(chain A and (resid 2 through 6 or resid 8...A11 - 17
141(chain A and (resid 2 through 6 or resid 8...A19 - 49
151(chain A and (resid 2 through 6 or resid 8...A0
161(chain A and (resid 2 through 6 or resid 8...A59 - 60
171(chain A and (resid 2 through 6 or resid 8...A1 - 203
181(chain A and (resid 2 through 6 or resid 8...A70 - 75
191(chain A and (resid 2 through 6 or resid 8...A77 - 80
1101(chain A and (resid 2 through 6 or resid 8...A1 - 203
1111(chain A and (resid 2 through 6 or resid 8...A81 - 111
1121(chain A and (resid 2 through 6 or resid 8...A0
1131(chain A and (resid 2 through 6 or resid 8...A1 - 203
1141(chain A and (resid 2 through 6 or resid 8...A1 - 203
1151(chain A and (resid 2 through 6 or resid 8...A156 - 157
1161(chain A and (resid 2 through 6 or resid 8...A159 - 164
211(chain B and (resid 2 through 6 or resid 8...B2 - 6
221(chain B and (resid 2 through 6 or resid 8...B8 - 9
231(chain B and (resid 2 through 6 or resid 8...B11 - 17
241(chain B and (resid 2 through 6 or resid 8...B19 - 49
251(chain B and (resid 2 through 6 or resid 8...B59 - 60
261(chain B and (resid 2 through 6 or resid 8...B2 - 68
271(chain B and (resid 2 through 6 or resid 8...B70 - 75
281(chain B and (resid 2 through 6 or resid 8...B77 - 80
291(chain B and (resid 2 through 6 or resid 8...B82
2101(chain B and (resid 2 through 6 or resid 8...B1 - 205
2111(chain B and (resid 2 through 6 or resid 8...B1 - 205
2121(chain B and (resid 2 through 6 or resid 8...B1 - 205
2131(chain B and (resid 2 through 6 or resid 8...B1 - 205
2141(chain B and (resid 2 through 6 or resid 8...B136 - 154
2151(chain B and (resid 2 through 6 or resid 8...B156 - 157
2161(chain B and (resid 2 through 6 or resid 8...B159 - 164
311(chain C and (resid 2 through 6 or resid 8...C2 - 6
321(chain C and (resid 2 through 6 or resid 8...C8 - 9
331(chain C and (resid 2 through 6 or resid 8...C11 - 17
341(chain C and (resid 2 through 6 or resid 8...C19 - 49
351(chain C and (resid 2 through 6 or resid 8...C59 - 60
361(chain C and (resid 2 through 6 or resid 8...C2 - 68
371(chain C and (resid 2 through 6 or resid 8...C70 - 75
381(chain C and (resid 2 through 6 or resid 8...C77 - 80
391(chain C and (resid 2 through 6 or resid 8...C82
3101(chain C and (resid 2 through 6 or resid 8...C1 - 200
3111(chain C and (resid 2 through 6 or resid 8...C1 - 200
3121(chain C and (resid 2 through 6 or resid 8...C1 - 200
3131(chain C and (resid 2 through 6 or resid 8...C1 - 200
3141(chain C and (resid 2 through 6 or resid 8...C136 - 154
3151(chain C and (resid 2 through 6 or resid 8...C156 - 157
3161(chain C and (resid 2 through 6 or resid 8...C159 - 164
411(chain D and (resid 2 through 6 or resid 8...D2 - 6
421(chain D and (resid 2 through 6 or resid 8...D8 - 9
431(chain D and (resid 2 through 6 or resid 8...D0
441(chain D and (resid 2 through 6 or resid 8...D52
451(chain D and (resid 2 through 6 or resid 8...D52 - 68
461(chain D and (resid 2 through 6 or resid 8...D70 - 75
471(chain D and (resid 2 through 6 or resid 8...D70 - 75
481(chain D and (resid 2 through 6 or resid 8...D77 - 80
491(chain D and (resid 2 through 6 or resid 8...D1 - 201
4101(chain D and (resid 2 through 6 or resid 8...D1 - 201
4111(chain D and (resid 2 through 6 or resid 8...D1 - 201
4121(chain D and (resid 2 through 6 or resid 8...D1 - 201
4131(chain D and (resid 2 through 6 or resid 8...D136 - 154
4141(chain D and (resid 2 through 6 or resid 8...D156 - 157
4151(chain D and (resid 2 through 6 or resid 8...D159 - 164
511(chain E and (resid 2 through 6 or resid 8...E2 - 6
521(chain E and (resid 2 through 6 or resid 8...E8 - 9
531(chain E and (resid 2 through 6 or resid 8...E0
541(chain E and (resid 2 through 6 or resid 8...E52
551(chain E and (resid 2 through 6 or resid 8...E59 - 6068
561(chain E and (resid 2 through 6 or resid 8...E84
571(chain E and (resid 2 through 6 or resid 8...E82
581(chain E and (resid 2 through 6 or resid 8...E0
591(chain E and (resid 2 through 6 or resid 8...E113 - 122
5101(chain E and (resid 2 through 6 or resid 8...E1 - 202
5111(chain E and (resid 2 through 6 or resid 8...E132 - 134
5121(chain E and (resid 2 through 6 or resid 8...E156 - 157
5131(chain E and (resid 2 through 6 or resid 8...E159 - 164
611(chain F and (resid 2 through 6 or resid 8...F2 - 6
621(chain F and (resid 2 through 6 or resid 8...F8 - 9
631(chain F and (resid 2 through 6 or resid 8...F0
641(chain F and (resid 2 through 6 or resid 8...F52
651(chain F and (resid 2 through 6 or resid 8...F52 - 68
661(chain F and (resid 2 through 6 or resid 8...F70 - 75
671(chain F and (resid 2 through 6 or resid 8...F70 - 75
681(chain F and (resid 2 through 6 or resid 8...F77 - 80
691(chain F and (resid 2 through 6 or resid 8...F1 - 201
6101(chain F and (resid 2 through 6 or resid 8...F1 - 201
6111(chain F and (resid 2 through 6 or resid 8...F1 - 201
6121(chain F and (resid 2 through 6 or resid 8...F1 - 201
6131(chain F and (resid 2 through 6 or resid 8...F136 - 154
6141(chain F and (resid 2 through 6 or resid 8...F156 - 157
6151(chain F and (resid 2 through 6 or resid 8...F159 - 164
711(chain G and (resid 2 through 6 or resid 8...G2 - 6
721(chain G and (resid 2 through 6 or resid 8...G8 - 9
731(chain G and (resid 2 through 6 or resid 8...G11 - 17
741(chain G and (resid 2 through 6 or resid 8...G19 - 49
751(chain G and (resid 2 through 6 or resid 8...G0
761(chain G and (resid 2 through 6 or resid 8...G59 - 60
771(chain G and (resid 2 through 6 or resid 8...G1 - 200
781(chain G and (resid 2 through 6 or resid 8...G70 - 75
791(chain G and (resid 2 through 6 or resid 8...G77 - 80
7101(chain G and (resid 2 through 6 or resid 8...G1 - 200
7111(chain G and (resid 2 through 6 or resid 8...G81 - 111
7121(chain G and (resid 2 through 6 or resid 8...G0
7131(chain G and (resid 2 through 6 or resid 8...G1 - 200
7141(chain G and (resid 2 through 6 or resid 8...G1 - 200
7151(chain G and (resid 2 through 6 or resid 8...G156 - 157
7161(chain G and (resid 2 through 6 or resid 8...G159 - 164
811(chain H and (resid 2 through 6 or resid 8...H2 - 6
821(chain H and (resid 2 through 6 or resid 8...H8 - 9
831(chain H and (resid 2 through 6 or resid 8...H11 - 17
841(chain H and (resid 2 through 6 or resid 8...H19 - 49
851(chain H and (resid 2 through 6 or resid 8...H0
861(chain H and (resid 2 through 6 or resid 8...H59 - 60
871(chain H and (resid 2 through 6 or resid 8...H1 - 201
881(chain H and (resid 2 through 6 or resid 8...H70 - 75
891(chain H and (resid 2 through 6 or resid 8...H77 - 80
8101(chain H and (resid 2 through 6 or resid 8...H1 - 201
8111(chain H and (resid 2 through 6 or resid 8...H81 - 111
8121(chain H and (resid 2 through 6 or resid 8...H0
8131(chain H and (resid 2 through 6 or resid 8...H1 - 201
8141(chain H and (resid 2 through 6 or resid 8...H1 - 201
8151(chain H and (resid 2 through 6 or resid 8...H156 - 157
8161(chain H and (resid 2 through 6 or resid 8...H159 - 164

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Ferritin /


Mass: 19401.906 Da / Num. of mol.: 8 / Mutation: E65K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin

-
Non-polymers , 5 types, 498 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H42
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.4 M (NH4)2 SO4, 0.1M MES. pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 2.359→20.44 Å / Num. obs: 86438 / % possible obs: 99.8 % / Redundancy: 7.516 % / Biso Wilson estimate: 40.582 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.23 / Rrim(I) all: 0.248 / Χ2: 1.049 / Net I/σ(I): 8.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.36-2.57.6481.5311.3310561413863138090.4641.64599.6
2.5-2.677.6831.061.9510013913034130330.6651.138100
2.67-2.897.6670.6753.159321912160121590.8290.725100
2.89-3.167.6360.4075.258552711202112000.9330.438100
3.16-3.537.5150.2069.787644710176101730.9810.222100
3.53-4.087.4930.12415.3567501901290090.9920.133100
4.08-4.987.4090.0822.256686765376510.9960.086100
4.98-7.017.2730.09618.343568599559900.9950.10499.9
7.01-20.446.1450.0528.0420980350234140.9980.05597.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.82 Å48.25 Å
Translation7.82 Å48.25 Å

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.15.1_3469refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vlg

1vlg


Resolution: 2.359→20.44 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.61
RfactorNum. reflection% reflection
Rfree0.2365 2092 2.43 %
Rwork0.2011 --
obs0.2019 86126 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.23 Å2 / Biso mean: 51.2991 Å2 / Biso min: 28.16 Å2
Refinement stepCycle: final / Resolution: 2.359→20.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10936 0 320 442 11698
Biso mean--75.88 54.02 -
Num. residues----1312
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3088X-RAY DIFFRACTION4.943TORSIONAL
12B3088X-RAY DIFFRACTION4.943TORSIONAL
13C3088X-RAY DIFFRACTION4.943TORSIONAL
14D3088X-RAY DIFFRACTION4.943TORSIONAL
15E3088X-RAY DIFFRACTION4.943TORSIONAL
16F3088X-RAY DIFFRACTION4.943TORSIONAL
17G3088X-RAY DIFFRACTION4.943TORSIONAL
18H3088X-RAY DIFFRACTION4.943TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.359-2.41370.33271360.2993549199
2.4137-2.4740.36681390.3045608100
2.474-2.54080.32191380.28795539100
2.5408-2.61540.35071390.2825580100
2.6154-2.69960.29621400.26755583100
2.6996-2.79590.31231390.26365604100
2.7959-2.90750.28531390.23735566100
2.9075-3.03940.24941390.22435601100
3.0394-3.19910.25251400.22695603100
3.1991-3.39870.23481390.20245601100
3.3987-3.65970.23541400.17815626100
3.6597-4.02550.2041400.17355635100
4.0255-4.60220.17091410.14735664100
4.6022-5.77650.20061420.17395691100
5.7765-20.440.21571410.1809564296
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)
19.0432-5.9397-1.3479.25375.27573.8169-0.2649-0.0920.4052-0.36740.5126-1.1553-0.72130.3247-0.2920.37720.0883-0.08570.58340.02230.6148.024784.6062115.9064
20.870.38010.67670.41130.12350.80840.0915-0.1208-0.02380.1166-0.08870.01980.0971-0.0442-0.01120.3890.01530.02430.3153-0.02490.406823.320472.7795113.5054
31.4385-0.81260.62070.6381-0.30011.2946-0.04170.04190.1445-0.033-0.0180.0189-0.00190.05780.05640.33340.00250.03370.2998-0.01540.413919.340191.0399.5859
45.84774.13692.41054.15812.24411.7535-0.0037-0.3201-0.13970.0582-0.0074-0.241-0.0227-0.04570.07420.35090.0347-0.03190.36080.03150.410616.2474103.1533101.5379
54.72623.4280.84314.9257-0.21881.70660.6867-1.10450.77150.9053-0.77640.0239-0.13-0.06480.030.5614-0.0272-0.12550.6325-0.19260.907331.774107.1224115.0263
64.1248-3.18994.01368.88610.37735.7763-0.13270.0891.2832-0.1018-0.4618-0.9125-0.20890.5090.55930.588-0.1824-0.05510.5478-0.09660.676856.4335120.4302146.2028
70.4631.1121-0.29765.2472-0.49950.36210.2331-0.283-0.2290.3322-0.2736-0.30810.01840.17980.01760.33070.0178-0.0950.48330.00770.402952.974896.621154.5535
80.14791.5416-0.84555.8813-2.35881.7172-0.0006-0.03850.196-0.16680.26650.7672-0.0076-0.134-0.30820.34010.0101-0.07420.47170.01730.45244.099497.9457153.6045
90.54360.2217-0.41522.40710.28231.07920.0509-0.1049-0.02490.3982-0.12940.03840.0925-0.05690.07670.3726-0.0195-0.08730.4824-0.01050.427247.814298.1193163.1133
102.0395-1.6673-2.15362.20931.82832.2928-0.67020.0115-0.5830.4279-0.5782-0.43150.5840.36731.21090.59960.1013-0.10760.52620.01610.793448.647366.9476148.3783
110.87481.2170.16344.20130.10121.14770.10360.0093-0.0878-0.2384-0.1669-0.3213-0.04740.276-0.06250.28930.0061-0.02380.4085-0.00380.351152.314490.6965140.0028
120.47630.6750.28645.3061-2.59581.7994-0.0175-0.07380.0376-0.24130.22310.28830.0924-0.1758-0.27140.34150.0125-0.01670.42440.01950.450443.902189.6331141.9233
130.68260.59490.04372.1490.29460.85650.0326-0.0204-0.0784-0.2511-0.0505-0.08890.02530.09890.04270.3322-0.0008-0.0110.3990.00650.44148.910787.3232131.2828
142.89340.07730.31964.6021-1.95465.5817-0.2590.32220.3644-0.80130.79561.3896-0.0802-0.9031-0.40020.6895-0.0784-0.240.43720.13690.708940.1922108.5137126.6756
153.09752.35931.80954.2071-2.07756.03240.5079-0.8150.17631.1490.16850.4769-0.144-0.4789-0.46440.6341-0.0997-0.04230.63080.03710.519438.7403138.4228173.4337
160.5239-0.32-0.12850.3362-0.33571.7775-0.02220.00160.06870.0187-0.0062-0.03080.208-0.03990.05280.3755-0.08670.00860.3675-0.00260.440340.0791131.6237146.7638
171.1012-0.18120.72960.4681-1.36484.92020.0073-0.02540.17990.20580.1588-0.06-0.4537-0.29940.01020.4047-0.0387-0.01160.3686-0.04420.511626.952148.1573143.6112
180.6745-0.0367-1.2074-0.0939-0.22736.9382-0.04050.03050.04810.0478-0.06070.02330.0583-0.62630.10050.3793-0.09010.0110.4344-0.06390.472521.9429140.7518146.667
190.6014-0.00850.30970.2039-0.40490.9716-0.0273-0.0770.17350.1130.0663-0.1263-0.1997-0.0584-0.05310.3982-0.0285-0.01830.3566-0.06740.49918.35151.3451145.0884
202.7137-1.6401-1.87963.72391.94115.3034-0.0957-0.41650.10820.8034-0.04640.26930.5735-0.81820.14410.5754-0.06990.04690.8299-0.03410.49412.3397141.3451166.3383
219.69453.71161.72712.83221.94942.1957-0.2799-0.2547-1.25090.03310.4261-0.56670.7914-0.0123-0.13330.52270.0156-0.01150.6710.06510.611150.6599103.6357178.1784
221.506-0.4142-1.20040.32640.13130.99810.0904-0.1510.12660.0976-0.055-0.1104-0.12710.1165-0.06840.4969-0.0345-0.08940.4847-0.06080.383932.9968119.5014183.9536
232.8319-0.6361-1.42040.93760.92931.40430.19080.23450.3172-0.1428-0.12030.0208-0.2788-0.2177-0.04020.59750.0026-0.03970.5250.01620.401725.4176128.5831175.3975
244.5009-1.46082.03853.3866-2.72552.672-0.3658-0.35420.62010.4718-0.17790.4609-0.9889-0.46950.40080.68170.0096-0.01550.8141-0.07050.63616.2651121.832203.2856
252.5169-0.6578-1.00321.33270.39290.6064-0.1794-0.0594-0.2370.1586-0.00450.06090.11070.01180.14380.4734-0.0287-0.04920.47750.01090.299122.109108.2706192.2588
262.4938-0.5344-0.91341.7694-0.00861.5577-0.1817-0.2708-0.31460.1417-0.1061-0.04550.26090.20590.20970.521-0.0072-0.05880.58320.0730.392821.792100.4354200.2586
272.4733-2.7424-1.56823.96251.72851.07940.19330.2693-0.3993-0.7025-0.32070.2627-0.0061-0.06420.09870.5391-0.0210.01590.55720.05030.406415.118995.2578193.6983
282.0614-0.5391-1.22435.20530.40214.5126-0.16310.1675-0.5276-0.6541-0.4049-0.27310.71390.18410.53620.9137-0.08930.15760.6497-0.09660.816428.661686.3929180.1239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )A1 - 5
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 164 )A6 - 164
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 115 )B1 - 115
4X-RAY DIFFRACTION4chain 'B' and (resid 116 through 146 )B116 - 146
5X-RAY DIFFRACTION5chain 'B' and (resid 147 through 164 )B147 - 164
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 5 )C1 - 5
7X-RAY DIFFRACTION7chain 'C' and (resid 6 through 36 )C6 - 36
8X-RAY DIFFRACTION8chain 'C' and (resid 37 through 65 )C37 - 65
9X-RAY DIFFRACTION9chain 'C' and (resid 66 through 164 )C66 - 164
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 5 )D1 - 5
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 36 )D6 - 36
12X-RAY DIFFRACTION12chain 'D' and (resid 37 through 70 )D37 - 70
13X-RAY DIFFRACTION13chain 'D' and (resid 71 through 146 )D71 - 146
14X-RAY DIFFRACTION14chain 'D' and (resid 147 through 164 )D147 - 164
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 5 )E1 - 5
16X-RAY DIFFRACTION16chain 'E' and (resid 6 through 164 )E6 - 164
17X-RAY DIFFRACTION17chain 'F' and (resid 1 through 36 )F1 - 36
18X-RAY DIFFRACTION18chain 'F' and (resid 37 through 65 )F37 - 65
19X-RAY DIFFRACTION19chain 'F' and (resid 66 through 146 )F66 - 146
20X-RAY DIFFRACTION20chain 'F' and (resid 147 through 164 )F147 - 164
21X-RAY DIFFRACTION21chain 'G' and (resid 1 through 5 )G1 - 5
22X-RAY DIFFRACTION22chain 'G' and (resid 6 through 115 )G6 - 115
23X-RAY DIFFRACTION23chain 'G' and (resid 116 through 164 )G116 - 164
24X-RAY DIFFRACTION24chain 'H' and (resid 1 through 5 )H1 - 5
25X-RAY DIFFRACTION25chain 'H' and (resid 6 through 75 )H6 - 75
26X-RAY DIFFRACTION26chain 'H' and (resid 76 through 115 )H76 - 115
27X-RAY DIFFRACTION27chain 'H' and (resid 116 through 146 )H116 - 146
28X-RAY DIFFRACTION28chain 'H' and (resid 147 through 164 )H147 - 164

+
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