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- PDB-6hhs: MamM CTD E289D - Cadmium form -

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Basic information

Entry
Database: PDB / ID: 6hhs
TitleMamM CTD E289D - Cadmium form
Components
  • Magnetosome protein MamM, Cation efflux protein family
  • Probable C-terminal region of MamM CTD E289D - Cadmium form
KeywordsMETAL TRANSPORT / Cation diffusion facilitator / magnetotactic bacteria
Function / homology
Function and homology information


magnetosome membrane / monoatomic cation transmembrane transporter activity / iron ion transport / metal ion binding / plasma membrane
Similarity search - Function
Cation efflux protein, cytoplasmic domain / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBarber-Zucker, S. / Zarivach, R.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation 167/16 Israel
Israel Ministry of Science, Technology and Space Israel
CitationJournal: To Be Published
Title: MamM CTD E289D - Cadmium form
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnetosome protein MamM, Cation efflux protein family
B: Magnetosome protein MamM, Cation efflux protein family
C: Magnetosome protein MamM, Cation efflux protein family
D: Magnetosome protein MamM, Cation efflux protein family
E: Magnetosome protein MamM, Cation efflux protein family
F: Magnetosome protein MamM, Cation efflux protein family
G: Magnetosome protein MamM, Cation efflux protein family
M: Probable C-terminal region of MamM CTD E289D - Cadmium form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,49933
Polymers83,9738
Non-polymers2,52625
Water2,036113
1
A: Magnetosome protein MamM, Cation efflux protein family
D: Magnetosome protein MamM, Cation efflux protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,93013
Polymers23,7932
Non-polymers1,13711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Magnetosome protein MamM, Cation efflux protein family
G: Magnetosome protein MamM, Cation efflux protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0795
Polymers23,7932
Non-polymers2873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Magnetosome protein MamM, Cation efflux protein family
E: Magnetosome protein MamM, Cation efflux protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,72111
Polymers23,7932
Non-polymers9289
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Magnetosome protein MamM, Cation efflux protein family
hetero molecules

F: Magnetosome protein MamM, Cation efflux protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1416
Polymers23,7932
Non-polymers3484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
5
M: Probable C-terminal region of MamM CTD E289D - Cadmium form


  • defined by author
  • 699 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6991
Polymers6991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.599, 94.545, 107.490
Angle α, β, γ (deg.)90.00, 91.76, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-407-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYAA214 - 2944 - 84
21METMETGLYGLYBB214 - 2944 - 84
12HISHISGLUGLUAA213 - 2923 - 82
22HISHISGLUGLUCC213 - 2923 - 82
13HISHISGLUGLUAA213 - 2923 - 82
23HISHISGLUGLUDD213 - 2923 - 82
14HISHISGLUGLUAA213 - 2923 - 82
24HISHISGLUGLUEE213 - 2923 - 82
15HISHISILEILEAA213 - 2933 - 83
25HISHISILEILEFF213 - 2933 - 83
16HISHISARGARGAA213 - 2913 - 81
26HISHISARGARGGG213 - 2913 - 81
17METMETGLUGLUBB214 - 2924 - 82
27METMETGLUGLUCC214 - 2924 - 82
18METMETGLUGLUBB214 - 2924 - 82
28METMETGLUGLUDD214 - 2924 - 82
19METMETGLUGLUBB214 - 2924 - 82
29METMETGLUGLUEE214 - 2924 - 82
110METMETILEILEBB214 - 2934 - 83
210METMETILEILEFF214 - 2934 - 83
111METMETARGARGBB214 - 2914 - 81
211METMETARGARGGG214 - 2914 - 81
112HISHISGLUGLUCC213 - 2923 - 82
212HISHISGLUGLUDD213 - 2923 - 82
113HISHISGLUGLUCC213 - 2923 - 82
213HISHISGLUGLUEE213 - 2923 - 82
114HISHISGLUGLUCC213 - 2923 - 82
214HISHISGLUGLUFF213 - 2923 - 82
115HISHISARGARGCC213 - 2913 - 81
215HISHISARGARGGG213 - 2913 - 81
116SERSERGLUGLUDD212 - 2922 - 82
216SERSERGLUGLUEE212 - 2922 - 82
117HISHISGLUGLUDD213 - 2923 - 82
217HISHISGLUGLUFF213 - 2923 - 82
118HISHISARGARGDD213 - 2913 - 81
218HISHISARGARGGG213 - 2913 - 81
119HISHISGLUGLUEE213 - 2923 - 82
219HISHISGLUGLUFF213 - 2923 - 82
120HISHISARGARGEE213 - 2913 - 81
220HISHISARGARGGG213 - 2913 - 81
121HISHISARGARGFF213 - 2913 - 81
221HISHISARGARGGG213 - 2913 - 81

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGM

#1: Protein
Magnetosome protein MamM, Cation efflux protein family / MamM protein


Mass: 11896.372 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: The MamM CTD E289D protein was the only protein in crystallization drop. The M chain is probably a C-terminal tail of one of the MamM CTD E289D monomers, however, it cannot be associated ...Details: The MamM CTD E289D protein was the only protein in crystallization drop. The M chain is probably a C-terminal tail of one of the MamM CTD E289D monomers, however, it cannot be associated with any of chains A-G and the density map does not allow to assign the exact residues to the short peptide that its backbone is clearly observable in the density map. Therefore, a Poly-Ala sequence was fitted into the map and the alignment displayed here is incorrect (alignment is actually not avavilable).
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: mamM, mgI491, MGR_4095 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Protein/peptide Probable C-terminal region of MamM CTD E289D - Cadmium form


Mass: 698.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The MamM CTD E289D protein was the only protein in crystallization drop. The M chain is probably a C-terminal tail of one of the MamM CTD E289D monomers, however, it cannot be associated ...Details: The MamM CTD E289D protein was the only protein in crystallization drop. The M chain is probably a C-terminal tail of one of the MamM CTD E289D monomers, however, it cannot be associated with any of chains A-G and the density map does not allow to assign the exact residues to the short peptide that its backbone is clearly observable in the density map. Therefore, a Poly-Ala sequence was fitted into the map and the alignment displayed here is incorrect (alignment is actually not avavilable).
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta

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Non-polymers , 4 types, 138 molecules

#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M (NH4)2SO4, 0.1M BIS-TRIS pH=6.5, 0.1M NaCl, 1.7mM CdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→47.27 Å / Num. obs: 22985 / % possible obs: 99.3 % / Redundancy: 6.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.273 / Net I/σ(I): 5.7
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2990 / CC1/2: 0.639 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X
Resolution: 2.7→47.27 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.835 / SU B: 25.817 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R: 0.9 / ESU R Free: 0.374 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29043 1140 5 %RANDOM
Rwork0.24964 ---
obs0.25167 21606 98.26 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 37.972 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å2-0 Å2-0.45 Å2
2---2.25 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.7→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4516 0 73 113 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0144633
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174155
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.6566261
X-RAY DIFFRACTIONr_angle_other_deg0.8561.6389712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89520.722291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67415782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.371557
X-RAY DIFFRACTIONr_chiral_restr0.0710.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025309
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02751
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_mcbond_it0.91.7892342
X-RAY DIFFRACTIONr_mcbond_other0.91.7892341
X-RAY DIFFRACTIONr_mcangle_it1.5692.6732914
X-RAY DIFFRACTIONr_mcangle_other1.5692.6732915
X-RAY DIFFRACTIONr_scbond_it1.4231.9452290
X-RAY DIFFRACTIONr_scbond_other1.4231.9452291
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5362.8663346
X-RAY DIFFRACTIONr_long_range_B_refined3.92521.1124852
X-RAY DIFFRACTIONr_long_range_B_other3.92521.1164853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A22580.08
12B22580.08
21A22810.07
22C22810.07
31A22680.08
32D22680.08
41A22710.09
42E22710.09
51A22910.08
52F22910.08
61A22030.09
62G22030.09
71B22310.09
72C22310.09
81B22290.09
82D22290.09
91B22000.1
92E22000.1
101B22190.1
102F22190.1
111B21960.09
112G21960.09
121C22610.09
122D22610.09
131C22600.09
132E22600.09
141C22820.07
142F22820.07
151C22200.11
152G22200.11
161D22840.09
162E22840.09
171D22760.08
172F22760.08
181D22060.1
182G22060.1
191E22910.08
192F22910.08
201E21890.12
202G21890.12
211F21930.11
212G21930.11
LS refinement shellResolution: 2.697→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 72 -
Rwork0.311 1490 -
obs--93.31 %
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)
12.4883-0.82160.37316.81471.96242.5428-0.1002-0.0592-0.26410.0734-0.0260.26220.0686-0.07220.12620.0089-0.00960.01970.26020.03020.0574-1.3538.977-11.497
23.3269-1.11230.2816.21720.04360.48390.09240.35420.0239-0.35120.0174-0.2925-0.09940.1672-0.10980.0452-0.0530.04510.3567-0.02320.097416.64432.726-25.416
36.09060.74112.06053.94450.8761.27680.2233-0.20350.23020.1454-0.12620.05090.0223-0.0072-0.09710.0380.01150.05920.27180.01010.1104-30.33250.837-17.231
46.84720.96951.89372.5370.33932.48610.08790.36760.0885-0.2876-0.0684-0.1689-0.10330.0552-0.01960.07120.02680.05490.24310.05380.0536-10.02951.922-26.36
51.34280.1239-0.45586.1409-2.6072.94670.0020.2806-0.2346-0.1756-0.0842-0.1220.11070.25520.08210.01780.01320.01250.2929-0.09520.0821-33.22830.484-23.546
63.0674-0.27450.47992.00842.16523.95930.0541-0.111-0.01-0.17930.0221-0.1862-0.09350.2858-0.07620.02250.00980.02150.24770.05050.1033-34.72626.1878.028
71.95370.13081.24585.83040.36886.67510.03050.50240.1864-0.6564-0.10520.0012-0.27810.06270.07470.1161-0.0420.05480.3801-0.07810.09925.02621.81-38.654
812.44492.7432.60920.60630.57620.5518-0.18680.44080.0204-0.04240.1330.0152-0.04920.09470.05380.33810.05820.02820.32390.05590.29194.37761.833-33.429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A213 - 295
2X-RAY DIFFRACTION2B214 - 301
3X-RAY DIFFRACTION3C213 - 293
4X-RAY DIFFRACTION4D211 - 293
5X-RAY DIFFRACTION5E212 - 293
6X-RAY DIFFRACTION6F213 - 294
7X-RAY DIFFRACTION7G213 - 292
8X-RAY DIFFRACTION8M7 - 14

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