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- PDB-2va0: Differential regulation of the xylan degrading apparatus of Cellv... -

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Basic information

Entry
Database: PDB / ID: 2va0
TitleDifferential regulation of the xylan degrading apparatus of Cellvibrio japonicus by a novel two component system
ComponentsABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
KeywordsTRANSFERASE / KINASE / PAS DOMAIN
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020
Similarity search - Function
Beta-Lactamase - #160 / Sensor histidine kinase (AbfS), sensor domain / Sensor histidine kinase (AbfS) sensor domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...Beta-Lactamase - #160 / Sensor histidine kinase (AbfS), sensor domain / Sensor histidine kinase (AbfS) sensor domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Histidine kinase
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.602 Å
AuthorsMurray, J.W. / Emami, K. / Topakas, E. / Nagy, T. / Henshaw, J. / Jackson, K.A. / Nelson, K.E. / Mongodin, E.F. / Lewis, R.J. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Regulation of the Xylan-Degrading Apparatus of Cellvibrio Japonicus by a Novel Two-Component System.
Authors: Emami, K. / Topakas, E. / Nagy, T. / Henshaw, J. / Jackson, K.A. / Nelson, K.E. / Mongodin, E.F. / Murray, J.W. / Lewis, R.J. / Gilbert, H.J.
History
DepositionAug 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Sep 28, 2011Group: Atomic model / Derived calculations
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
B: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
C: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
D: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
E: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
F: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,94815
Polymers92,2726
Non-polymers6769
Water1,910106
1
A: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5093
Polymers15,3791
Non-polymers1302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4742
Polymers15,3791
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5093
Polymers15,3791
Non-polymers1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4742
Polymers15,3791
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4742
Polymers15,3791
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5093
Polymers15,3791
Non-polymers1302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.772, 80.014, 101.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAA49 - 527 - 10
21ASPASPLYSLYSBB47 - 525 - 10
31ASPASPLYSLYSCC48 - 526 - 10
41SERSERLYSLYSDD49 - 527 - 10
51SERSERLYSLYSEE49 - 527 - 10
61SERSERLYSLYSFF49 - 527 - 10
12LEULEULEULEUAA54 - 5512 - 13
22LEULEULEULEUBB54 - 5512 - 13
32LEULEULEULEUCC54 - 5512 - 13
42LEULEULEULEUDD54 - 5512 - 13
52LEULEULEULEUEE54 - 5512 - 13
62LEULEULEULEUFF54 - 5512 - 13
13METMETGLYGLYAA58 - 6016 - 18
23METMETGLYGLYBB58 - 6016 - 18
33METMETGLYGLYCC58 - 6016 - 18
43METMETGLYGLYDD58 - 6016 - 18
53METMETGLYGLYEE58 - 6016 - 18
63METMETGLYGLYFF58 - 6016 - 18
14ALAALATHRTHRAA62 - 6720 - 25
24ALAALATHRTHRBB62 - 6720 - 25
34ALAALATHRTHRCC62 - 6720 - 25
44ALAALATHRTHRDD62 - 6720 - 25
54ALAALATHRTHREE62 - 6720 - 25
64ALAALATHRTHRFF62 - 6720 - 25
15GLNGLNASNASNAA69 - 7927 - 37
25GLNGLNASNASNBB69 - 7927 - 37
35GLNGLNASNASNCC69 - 7927 - 37
45GLNGLNASNASNDD69 - 7927 - 37
55GLNGLNASNASNEE69 - 7927 - 37
65GLNGLNASNASNFF69 - 7927 - 37
16SERSERLEULEUAA81 - 8239 - 40
26SERSERLEULEUBB81 - 8239 - 40
36SERSERLEULEUCC81 - 8239 - 40
46SERSERLEULEUDD81 - 8239 - 40
56SERSERLEULEUEE81 - 8239 - 40
66SERSERLEULEUFF81 - 8239 - 40
17PHEPHEASPASPAA84 - 8942 - 47
27PHEPHEASPASPBB84 - 8942 - 47
37PHEPHEASPASPCC84 - 8942 - 47
47PHEPHEASPASPDD84 - 8942 - 47
57PHEPHEASPASPEE84 - 8942 - 47
67PHEPHEASPASPFF84 - 8942 - 47
18ASNASNARGARGAA91 - 12349 - 81
28ASNASNARGARGBB91 - 12349 - 81
38ASNASNARGARGCC91 - 12349 - 81
48ASNASNARGARGDD91 - 12349 - 81
58ASNASNARGARGEE91 - 12349 - 81
68ASNASNARGARGFF91 - 12349 - 81
19LEULEUGLYGLYAA127 - 13785 - 95
29LEULEUGLYGLYBB127 - 13785 - 95
39LEULEUGLYGLYCC127 - 13785 - 95
49LEULEUGLYGLYDD127 - 13785 - 95
59LEULEUGLYGLYEE127 - 13785 - 95
69LEULEUGLYGLYFF127 - 13785 - 95
110SERSERSERSERAA139 - 14697 - 104
210SERSERSERSERBB139 - 14697 - 104
310SERSERSERSERCC139 - 14697 - 104
410SERSERSERSERDD139 - 14697 - 104
510SERSERSERSEREE139 - 14697 - 104
610SERSERSERSERFF139 - 14697 - 104

NCS oper:
IDCodeMatrixVector
1given(0.07, 0.995, -0.07), (0.99, -0.077, -0.117), (-0.122, -0.062, -0.991)7.8496, 5.155, 141.21254
2given(0.52754, -0.8495, 0.00684), (0.84948, 0.52758, 0.00583), (-0.00856, 0.00274, 0.99996)-0.49595, 0.10939, 34.11854
3given(0.88582, 0.45917, -0.06696), (0.45274, -0.88687, -0.09215), (-0.1017, 0.05132, -0.99349)5.55003, 0.13241, 107.39598
4given(-0.50049, -0.86555, 0.01829), (0.86569, -0.50057, -0.00024), (0.00937, 0.01571, 0.99983)-0.31278, -0.22044, 68.19968
5given(0.82362, -0.56216, -0.07503), (-0.56713, -0.81721, -0.10266), (-0.0036, 0.12711, -0.99188)2.86134, -2.97708, 73.81616

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Components

#1: Protein
ABFS ARABINOFURANOSIDASE TWO COMPONENT SYSTEM SENSOR PROTEIN / SENSOR HISTIDINE KINASE A / ABFS


Mass: 15378.591 Da / Num. of mol.: 6 / Fragment: SENSOR DOMAIN, RESIDUES 44-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3PFT7
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTIFR ORF ORF03629 RELEASED AS UNP B3PFT7 . RESIDUES 166 TO 173 CORRESPOND TO A C-TERMINAL HIS-TAG.

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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: 3 Å3/Da / Density % sol: 59 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97857
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.6→37.56 Å / Num. obs: 27726 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.69 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 3.06
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.34 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.602→37.037 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 19.879 / SU ML: 0.213 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.538 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1430 5.24 %RANDOM
Rwork0.1994 ---
obs0.202 27692 99.849 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 9.255 Å2
Baniso -1Baniso -2Baniso -3
1-0.514 Å20 Å20 Å2
2--0.178 Å20 Å2
3----0.692 Å2
Refinement stepCycle: LAST / Resolution: 2.602→37.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5151 0 33 106 5290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225274
X-RAY DIFFRACTIONr_bond_other_d0.0020.023728
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9727146
X-RAY DIFFRACTIONr_angle_other_deg1.11139032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4555627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46123.103261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94315957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7321563
X-RAY DIFFRACTIONr_chiral_restr0.1010.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025730
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021045
X-RAY DIFFRACTIONr_nbd_refined0.2350.21130
X-RAY DIFFRACTIONr_nbd_other0.2150.23809
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22523
X-RAY DIFFRACTIONr_nbtor_other0.0940.23017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9611.54049
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15825180
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.97732381
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8864.51966
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A499tight positional0.050.05
2B499tight positional0.070.05
3C499tight positional0.070.05
4D499tight positional0.060.05
5E499tight positional0.060.05
6F499tight positional0.050.05
1A640medium positional0.320.5
2B640medium positional0.30.5
3C640medium positional0.270.5
4D640medium positional0.260.5
5E640medium positional0.330.5
6F640medium positional0.280.5
1A499tight thermal0.110.5
2B499tight thermal0.140.5
3C499tight thermal0.140.5
4D499tight thermal0.120.5
5E499tight thermal0.110.5
6F499tight thermal0.10.5
1A640medium thermal0.522
2B640medium thermal0.622
3C640medium thermal0.582
4D640medium thermal0.532
5E640medium thermal0.512
6F640medium thermal0.522
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 94 -
Rwork0.286 1905 -
obs--99.95 %
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)
13.689-0.3937-2.78022.8595-0.30644.6937-0.0266-0.68030.06840.54890.0127-0.3663-0.09370.74140.01390.01040.0196-0.11960.2217-0.025-0.009218.4276.08181.29
22.3415-0.63150.30954.05160.59442.80680.0719-0.10910.10220.0480.02340.015-0.00790.0244-0.0953-0.2278-0.0089-0.004-0.0767-0.0317-0.07729.19614.08758.401
33.3482-0.8458-0.31943.44530.64112.55320.0127-0.235-0.20350.03250.0607-0.11720.07150.0834-0.0734-0.24570.0183-0.0208-0.09920.0371-0.025914.711-12.71247.328
42.35250.3131.48514.33010.4224.0947-0.0290.25940.1023-0.41370.0363-0.4433-0.27460.441-0.0073-0.0746-0.01030.0387-0.07440.0073-0.012716.687-0.66824.553
51.93890.44790.5983.95661.10072.96130.0569-0.031-0.1039-0.0184-0.10470.16040.3646-0.11410.04780.1215-0.0056-0.0355-0.13730.0109-0.0649-3.827-19.20813.447
63.75241.07871.02561.7366-0.84465.1420.05990.4469-0.2765-0.0086-0.0093-0.1370.28030.4083-0.05060.15260.1197-0.01040.0311-0.0248-0.05847.705-15.164-9.519
79.29742.9305-8.44177.2036-3.050321.74540.07990.23670.31790.12020.0406-0.3129-0.0891-0.4808-0.1205-0.2226-0.067-0.0213-0.0779-0.01730.067122.80524.07154.035
83.9433-2.4995-0.401515.97912.81464.40430.3903-0.4012-0.08880.0833-0.45090.31540.33820.01150.06060.27750.01340.045-0.35730.08490.0496-2.543-41.35718.021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 147
2X-RAY DIFFRACTION2B47 - 147
3X-RAY DIFFRACTION3C48 - 146
4X-RAY DIFFRACTION4D49 - 146
5X-RAY DIFFRACTION5E49 - 147
6X-RAY DIFFRACTION6F49 - 147
7X-RAY DIFFRACTION7B151 - 168
8X-RAY DIFFRACTION8E148 - 168

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