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- PDB-2f1m: Conformational flexibility in the multidrug efflux system protein AcrA -

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Basic information

Entry
Database: PDB / ID: 2f1m
TitleConformational flexibility in the multidrug efflux system protein AcrA
ComponentsAcriflavine resistance protein A
KeywordsTRANSPORT PROTEIN / helical hairpin / lipoyl domain / beta barrel
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic transport / bile acid and bile salt transport / transmembrane transporter activity / outer membrane-bounded periplasmic space / response to antibiotic / identical protein binding
Similarity search - Function
Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Multidrug efflux pump subunit AcrA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.71 Å
AuthorsMikolosko, J. / Bobyk, K. / Zgurskaya, H.I. / Ghosh, P.
CitationJournal: Structure / Year: 2006
Title: Conformational Flexibility in the Multidrug Efflux System Protein AcrA.
Authors: Mikolosko, J. / Bobyk, K. / Zgurskaya, H.I. / Ghosh, P.
History
DepositionNov 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acriflavine resistance protein A
B: Acriflavine resistance protein A
C: Acriflavine resistance protein A
D: Acriflavine resistance protein A


Theoretical massNumber of molelcules
Total (without water)121,4214
Polymers121,4214
Non-polymers00
Water64936
1
A: Acriflavine resistance protein A
B: Acriflavine resistance protein A


Theoretical massNumber of molelcules
Total (without water)60,7102
Polymers60,7102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-9 kcal/mol
Surface area24990 Å2
MethodPISA
2
C: Acriflavine resistance protein A
D: Acriflavine resistance protein A


Theoretical massNumber of molelcules
Total (without water)60,7102
Polymers60,7102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-8 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.788, 100.031, 332.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
53A
63B
73C
83D
14A
24B
34C
44D
15A
25B
35C
45D
16A
26B
36C
46D
17A
27B
37C
47D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRALA6AA54 - 6211 - 19
211THRALA6BB54 - 6211 - 19
311THRALA6CC54 - 6211 - 19
411THRALA6DD54 - 6211 - 19
112ARGILE3AA64 - 9621 - 53
212ARGILE3BB64 - 9621 - 53
312ARGILE3CC64 - 9621 - 53
412ARGILE3DD64 - 9621 - 53
113ALALYS5AA99 - 13156 - 88
213ALALYS5BB99 - 13156 - 88
313ALALYS5CC99 - 13156 - 88
413ALALYS5DD99 - 13156 - 88
523GLNLYS4AA141 - 17598 - 132
623GLNLYS4BB141 - 17598 - 132
723GLNLYS4CC141 - 17598 - 132
823GLNLYS4DD141 - 17598 - 132
114VALGLN3AA176 - 208133 - 165
214VALGLN3BB176 - 208133 - 165
314VALGLN3CC176 - 208133 - 165
414VALGLN3DD176 - 208133 - 165
115LEUGLN5AA209 - 218166 - 175
215LEUGLN5BB209 - 218166 - 175
315LEUGLN5CC209 - 218166 - 175
415LEUGLN5DD209 - 218166 - 175
116ALAASP5AA242 - 257199 - 214
216ALAASP5BB242 - 257199 - 214
316GLYASP5CC240 - 257197 - 214
416GLYASP5DD240 - 257197 - 214
117THRLEU5AA275 - 297232 - 254
217THRLEU5BB275 - 297232 - 254
317THRLEU5CC275 - 297232 - 254
417THRLEU5DD275 - 297232 - 254

NCS ensembles :
ID
1
2
3
4
5
6
7
DetailsThe current oligomerization state of AcrA is unknown.

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Components

#1: Protein
Acriflavine resistance protein A


Mass: 30355.184 Da / Num. of mol.: 4 / Fragment: residues 45-312 / Mutation: F223M, L224M, L287M, L288M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: acrA, lir, mtcA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P0AE06
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 277 K / pH: 5.4
Details: 30% 2-methyl-2,4-pentadiol (MPD), 20 mM MgCl2, 100 mM citrate pH 5.4, 1 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.40

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2004
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection

D res low: 50 Å / % possible obs: 99.8

Redundancy (%)IDNumberRmerge(I) obsΧ2D res high (Å)
4.21573520.1391.0323
4.42410310.0981.0423.39
4.23372760.1851.0493.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465098.410.041.0354.3
5.136.4610010.0841.0074.4
4.485.1310010.0871.0284.4
4.074.4810010.1261.0294.4
3.784.0710010.1911.044.5
3.563.7810010.2461.0434.4
3.383.5699.910.3641.0624.3
3.233.3899.910.5171.0374.1
3.113.2399.910.6371.0153.8
33.1199.710.7161.0163.4
7.35098.220.0341.0344.3
5.797.310020.0661.0374.4
5.065.7910020.0741.0384.4
4.65.0610020.0771.0574.5
4.274.610020.0941.0634.5
4.024.2710020.1311.0684.5
3.824.0210020.1711.0384.5
3.653.8210020.2071.0454.5
3.513.6599.920.2771.034.5
3.393.5199.920.3891.0084.5
7.53509830.0461.0484.3
5.987.5310030.1341.0684.3
5.235.9899.930.1711.0554.4
4.755.2310030.1641.0384.4
4.414.7510030.2071.0634.3
4.154.4110030.2541.0544.2
3.944.1510030.311.0334.1
3.773.9410030.3941.0454.1
3.633.7799.930.4461.0593.9
3.53.6399.930.5341.0193.8
ReflectionResolution: 2.7→50 Å / Num. obs: 39324 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.3 / % possible all: 91.1

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
128.608-49.811216.176SE3001.61
224.466-42.925215.138SE225.171.39
363.96713.11151.932SE81.791.72
422.30170.87954.6SE109.951.84
5-1.42726.768185.307SE188.640.96
610.50341.74865.087SE139.462.1
75.87737.10159.211SE89.521.85
86.43841.56264.423SE161.012.11
9-34.29130.375192.897SE132.061.45
1085.58920.69422.854SE120.191.95
115.43977.61229.71SE124.272.05
12-9.19723.051185.722SE203.250.63
1312.74479.66426.125SE132.562.26
1426.19618.13121.567SE87.582.16
1521.79515.51728.129SE91.692.17
1625.73314.31122.663SE136.242.07
1734.40825.932140.401SE117.851.85
1825.69418.182110.017SE124.081.95
1926.914-10.026229.861SE263.621.08
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 30180
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
11.93-10051.30.891501
9.47-11.93400.937501
8.18-9.4746.60.931565
7.31-8.1845.30.925616
6.66-7.3147.40.911690
6.16-6.6648.20.896738
5.76-6.1652.30.888815
5.43-5.7651.90.899842
5.15-5.4353.10.896861
4.91-5.1557.60.918936
4.7-4.9158.20.913981
4.51-4.759.40.9131002
4.35-4.5162.60.9191069
4.2-4.3567.90.911046
4.07-4.268.10.8951147
3.95-4.0769.60.8981133
3.83-3.9574.90.911205
3.73-3.8374.80.8881184
3.64-3.7376.10.891313
3.55-3.6480.80.891238
3.47-3.5581.90.8671329
3.39-3.4784.50.8421332
3.32-3.3986.30.7991396
3.25-3.3285.30.7911388
3.19-3.2586.50.7491376
3.13-3.1988.40.7391504
3.07-3.1390.20.711449
3-3.0788.50.6262023

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.71→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.905 / SU B: 29.458 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.563 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1972 5 %RANDOM
Rwork0.237 ---
all0.239 40642 --
obs0.239 39271 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.96 Å2
Baniso -1Baniso -2Baniso -3
1--6.28 Å20 Å20 Å2
2--10.54 Å20 Å2
3----4.26 Å2
Refinement stepCycle: LAST / Resolution: 2.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6964 0 0 36 7000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226988
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9619506
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.72725.369298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.903151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1131539
X-RAY DIFFRACTIONr_chiral_restr0.0980.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025251
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.22844
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.24811
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.2102
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3521.54680
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.61627368
X-RAY DIFFRACTIONr_scbond_it1.06232538
X-RAY DIFFRACTIONr_scangle_it1.7354.52138
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21A132tight positional0.040.05
22B132tight positional0.040.05
23C132tight positional0.040.05
24D132tight positional0.030.05
41A132tight positional0.040.05
42B132tight positional0.040.05
43C132tight positional0.050.05
44D132tight positional0.040.05
31A386medium positional0.530.5
32B386medium positional0.710.5
33C386medium positional0.730.5
34D386medium positional0.40.5
51A40medium positional0.470.5
52B40medium positional0.290.5
53C40medium positional0.390.5
54D40medium positional0.310.5
61A64medium positional0.740.5
62B64medium positional0.370.5
63C64medium positional0.40.5
64D64medium positional0.380.5
71A92medium positional0.420.5
72B92medium positional0.30.5
73C92medium positional0.330.5
74D92medium positional0.240.5
11A64loose positional0.655
12B64loose positional0.935
13C64loose positional0.555
14D64loose positional0.735
21A119loose positional0.495
22B119loose positional0.545
23C119loose positional0.555
24D119loose positional0.785
31A113loose positional0.645
32B113loose positional1.035
33C113loose positional0.845
34D113loose positional0.875
41A94loose positional0.475
42B94loose positional0.555
43C94loose positional0.475
44D94loose positional0.55
51A41loose positional0.755
52B41loose positional0.625
53C41loose positional0.845
54D41loose positional0.775
61A48loose positional1.785
62B48loose positional0.855
63C48loose positional0.895
64D48loose positional0.935
71A87loose positional1.065
72B87loose positional0.945
73C87loose positional0.675
74D87loose positional0.745
21A132tight thermal1.35
22B132tight thermal1.065
23C132tight thermal1.535
24D132tight thermal1.545
41A132tight thermal1.945
42B132tight thermal1.435
43C132tight thermal1.215
44D132tight thermal1.015
31A386medium thermal1.9510
32B386medium thermal2.3210
33C386medium thermal1.710
34D386medium thermal2.710
51A40medium thermal3.6710
52B40medium thermal4.5710
53C40medium thermal1.610
54D40medium thermal1.6810
61A64medium thermal3.0710
62B64medium thermal1.9910
63C64medium thermal1.5510
64D64medium thermal2.0110
71A92medium thermal1.9410
72B92medium thermal1.1710
73C92medium thermal2.1910
74D92medium thermal2.7110
11A64loose thermal4.1320
12B64loose thermal5.6120
13C64loose thermal3.7220
14D64loose thermal1.8720
21A119loose thermal2.4520
22B119loose thermal2.4420
23C119loose thermal2.3920
24D119loose thermal2.0320
31A113loose thermal2.3320
32B113loose thermal3.9420
33C113loose thermal2.2520
34D113loose thermal3.4220
41A94loose thermal2.6320
42B94loose thermal2.3520
43C94loose thermal1.7620
44D94loose thermal1.7320
51A41loose thermal4.6120
52B41loose thermal5.120
53C41loose thermal2.2320
54D41loose thermal2.0120
61A48loose thermal3.220
62B48loose thermal2.5420
63C48loose thermal1.520
64D48loose thermal2.0420
71A87loose thermal2.1820
72B87loose thermal1.5420
73C87loose thermal2.6420
74D87loose thermal3.220
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 129 -
Rwork0.407 2329 -
obs--81.23 %
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)
12.5622.4472-0.448810.7774-3.99021.80740.0692-0.20060.12230.5708-0.06650.4914-0.0531-0.217-0.00270.0801-0.03390.0038-0.1324-0.0893-0.200529.011-5.386205.401
23.39080.9159-2.54575.5654-4.16328.03370.2037-0.6450.26780.8945-0.05980.1494-0.65530.538-0.1440.1506-0.0478-0.0363-0.1486-0.1197-0.075140.06715.894209.701
38.2369-0.14822.91151.0435-0.16983.6420.10950.7262-0.1144-0.12380.12720.13010.0490.3582-0.23670.2054-0.0244-0.0092-0.2589-0.0187-0.15740.82225.506210.613
43.9579-0.46012.36992.36951.633212.0963-0.02810.8780.58310.07380.046-0.352-0.28361.3961-0.01790.1596-0.05870.01470.139-0.03230.060423.4834.449210.513
51.54820.47832.68761.01040.605623.9938-0.03080.5691-0.2496-0.2016-0.0746-0.1132-0.241-0.17860.10540.13410.0808-0.009-0.0554-0.0849-0.12128.098.651163.242
68.87670.42476.85181.57220.719912.5337-0.21170.51250.9439-0.4625-0.41370.3815-0.8996-0.95790.62540.35560.2167-0.057-0.05590.0252-0.012322.31323.736170.794
70.34550.206-0.48160.2359-1.956925.32730.029-0.227-0.04430.04020.02470.02290.2333-0.1202-0.05370.50340.2547-0.0384-0.0043-0.0041-0.1348.21421.72254.005
84.42821.7297-1.70764.2517-3.39859.7834-0.4546-0.8131-1.06490.7601-0.3379-0.63080.7581.09630.79250.61890.4499-0.05070.34350.0160.071123.68613.834249.3
911.7577-2.5657-0.04894.5456-5.023111.58250.2024-1.2141-1.93790.66370.40760.40721.6458-1.6077-0.610.6105-0.3943-0.07610.36820.27930.303120.626-33.158218.393
104.1812-6.3858-2.19716.3897-0.876711.5076-0.8284-0.7655-2.02571.98220.26311.13692.1159-0.48020.56531.0990.06620.38780.31820.18220.556926.81-1.237230.757
1119.2049-0.22465.22744.25420.29265.18320.5253.2075-0.4871-0.3444-0.31330.06840.19130.1008-0.21170.3290.0148-0.02610.4116-0.0753-0.0507-24.97722.447193.837
1230.1377-6.97160.9664.75730.27287.98050.17963.4496-0.9604-0.306-0.42451.70790.007-1.81780.24490.34550.03660.00711.148-0.19980.16747.76926.021185.817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA53 - 10010 - 57
2X-RAY DIFFRACTION2BB53 - 10010 - 57
3X-RAY DIFFRACTION2BB170 - 210127 - 167
4X-RAY DIFFRACTION3CC53 - 10010 - 57
5X-RAY DIFFRACTION3CC170 - 210127 - 167
6X-RAY DIFFRACTION4DD54 - 10011 - 57
7X-RAY DIFFRACTION4DD170 - 210127 - 167
8X-RAY DIFFRACTION5AA101 - 16958 - 126
9X-RAY DIFFRACTION6BB101 - 16958 - 126
10X-RAY DIFFRACTION7CC101 - 16958 - 126
11X-RAY DIFFRACTION8DD101 - 16958 - 126
12X-RAY DIFFRACTION9AA211 - 298168 - 255
13X-RAY DIFFRACTION10BB211 - 297168 - 254
14X-RAY DIFFRACTION11CC211 - 299168 - 256
15X-RAY DIFFRACTION12DD211 - 297168 - 254

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