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- PDB-2wqu: Internalin domain of Listeria monocytogenes InlB: triclinic cryst... -

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Basic information

Entry
Database: PDB / ID: 2wqu
TitleInternalin domain of Listeria monocytogenes InlB: triclinic crystal form
ComponentsINTERNALIN B
KeywordsCELL INVASION / HGF RECEPTOR LIGAND / LEUCINE RICH REPEAT / LRR / C-MET LIGAND / VIRULENCE FACTOR
Function / homology
Function and homology information


InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / cell surface / extracellular region / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal ...GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Internalin B / Internalin B
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNiemann, H.H. / Heinz, D.W.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Ligand-Mediated Dimerization of the met Receptor Tyrosine Kinase by the Bacterial Invasion Protein Inlb.
Authors: Ferraris, D.M. / Gherardi, E. / Di, Y. / Heinz, D.W. / Niemann, H.H.
History
DepositionAug 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: 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 / pdbx_initial_refinement_model / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERNALIN B
B: INTERNALIN B
C: INTERNALIN B
D: INTERNALIN B
E: INTERNALIN B
F: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,37226
Polymers193,4636
Non-polymers1,90920
Water1,09961
1
A: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6165
Polymers32,2441
Non-polymers3724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6285
Polymers32,2441
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3402
Polymers32,2441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: INTERNALIN B


Theoretical massNumber of molelcules
Total (without water)32,2441
Polymers32,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7246
Polymers32,2441
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8207
Polymers32,2441
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.660, 70.650, 124.660
Angle α, β, γ (deg.)74.47, 83.13, 85.65
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.83625, -0.52905, 0.14423), (-0.54805, 0.79762, -0.25189), (0.01822, -0.28969, -0.95695)58.20268, 17.40254, -0.28812
2given(0.84201, 0.52067, -0.14113), (-0.52807, 0.74205, -0.41292), (-0.11026, 0.42221, 0.89977)38.46272, 21.7145, -51.93545
3given(-0.99806, 0.0616, 0.00865), (0.06211, 0.99461, 0.08303), (-0.00349, 0.0834, -0.99651)1.68736, 0.25157, -0.45215
4given(0.64842, -0.61765, -0.44504), (0.56733, 0.00224, 0.82349), (-0.50763, -0.78645, 0.35186)53.24129, -29.90241, 67.21381
5given(-0.56188, 0.61861, 0.54919), (0.62709, -0.11444, 0.77049), (0.53949, 0.77732, -0.32362)49.56183, 6.49988, 0.71027

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Components

#1: Protein
INTERNALIN B


Mass: 32243.818 Da / Num. of mol.: 6 / Fragment: INTERNALIN DOMAIN, RESIDUES 36-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Plasmid: PETM30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS / References: UniProt: P25147, UniProt: P0DQD2*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND ...Details: SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 55139 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 4.96 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.13
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.59 / % possible all: 74.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6T
Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / SU B: 25.185 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2746 5 %RANDOM
Rwork0.191 ---
obs0.194 52393 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.41 Å2-0.01 Å2
2--2.07 Å2-0.38 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13226 0 103 61 13390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213534
X-RAY DIFFRACTIONr_bond_other_d0.0010.028974
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.99218376
X-RAY DIFFRACTIONr_angle_other_deg0.812322379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46551683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.21426.951574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.333152555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.21524
X-RAY DIFFRACTIONr_chiral_restr0.0540.22218
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022202
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_it0.1411.58421
X-RAY DIFFRACTIONr_mcbond_other0.0231.53359
X-RAY DIFFRACTIONr_mcangle_it0.28213761
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.48435113
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8374.54610
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
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 160 -
Rwork0.255 3070 -
obs--74.92 %
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)
15.2809-0.0255.0573.28550.53359.04210.0938-0.650.08170.6310.0512-0.04570.2325-0.4831-0.1450.23790.01430.01930.20530.08280.134119.22210.950644.7411
22.1253-1.433-0.10814.37-2.44078.3352-0.051-0.02530.18220.13640.0264-0.5176-0.2120.53990.02460.08930.0179-0.00060.14390.00080.162322.647814.60130.1473
31.6516-0.85961.0971.1921-0.71493.66380.0272-0.0098-0.0701-0.0730.04810.11690.10350.1135-0.07530.0263-0.0080.01860.00660.0320.117816.85818.01994.8349
415.6971-3.9487-1.59628.9299-4.6222.39550.50170.6370.5078-1.3118-0.41640.4485-0.1299-0.6693-0.08530.2570.1547-0.09880.28110.03170.12781.318631.4617-12.9935
58.0439-9.01392.3614.7733-2.11292.35780.13920.5098-0.79130.8817-0.48770.90450.3324-0.14280.34850.12320.00760.04290.18190.00880.07037.993117.4359-4.0357
65.01083.3213-0.2066.29810.70033.9066-0.09610.1725-0.3077-0.27190.1686-0.20740.25970.4417-0.07250.17350.02620.04270.1041-0.03860.193542.99512.4649-46.4148
74.23640.76931.63165.89062.64885.8884-0.1474-0.2461-0.0470.07860.03330.0759-0.17240.02910.11410.0533-0.00650.04590.15570.04610.036437.422310.444-34.3323
81.11840.21490.26591.54931.5297.3428-0.00520.1749-0.1154-0.029-0.04340.06810.059-0.05170.0486-0.01570.0196-0.00060.12090.03920.077934.026214.6749-14.9278
91.27310.0556-1.0128.9665-0.73014.9530.4058-0.39420.64190.0026-0.08510.687-1.45860.0238-0.32080.3914-0.0620.10520.2365-0.120.320836.878335.7568-0.1002
103.98990.230.290510.06981.95325.4610.1579-0.49530.55470.9951-0.1491-0.1407-1.07120.589-0.00880.3683-0.16920.11470.2477-0.08880.10340.441432.93950.7737
118.3036-2.7173-1.305413.0151-0.37184.6702-0.3208-0.6356-0.5090.60050.19810.12510.4731-0.20280.12270.1707-0.0430.05540.16830.03060.141853.726-0.7622-6.9606
122.8607-0.9161-0.26637.7991-1.23916.25120.11410.2044-0.1744-0.1524-0.13170.1431-0.08710.04450.01760.02620.03180.03950.23380.00470.064558.51938.3374-19.5599
131.13810.049-1.84613.7908-2.14255.9991-0.1161-0.0733-0.14770.08910.0243-0.18150.11350.33070.09190.01230.0258-0.01830.21080.02280.138564.367613.7576-32.8464
141.6609-0.0823-0.25485.5593-1.35716.1960.02770.32450.4032-0.01810.11990.0616-0.6088-0.2631-0.14760.06160.0350.00630.25510.08060.16859.786427.3737-46.7308
152.5939-0.7671.205612.041.04795.663-0.04840.27480.3812-0.5015-0.16280.4603-0.8732-0.41140.21120.28810.08280.04850.37920.13990.24155.378133.4981-51.3241
1610.34985.83464.80944.80362.040710.6977-0.7581.9311-0.4517-1.01880.730.0953-0.09211.51010.0280.4923-0.14950.02840.829-0.03940.213278.042919.472-100.9288
178.11742.30142.95673.35672.58099.2622-0.1791-0.01860.2036-0.4373-0.00830.2302-0.218-0.08430.18730.19530.01560.01610.18720.00160.125674.844820.5896-86.156
180.57710.3571-0.09392.5022-0.61095.79350.00580.0452-0.0273-0.1005-0.07310.16640.0996-0.50550.06730.0166-0.01080.00620.1728-0.00810.142474.958620.8955-64.1645
192.10261.23481.30142.64060.79832.8353-0.1420.00880.10010.00490.0866-0.1082-0.1575-0.10090.05540.08860.0514-0.01130.18170.0320.117487.283225.3719-46.0932
203.25274.38872.506613.00763.87156.1859-0.0917-0.1398-0.21390.10740.18-0.7505-0.08570.1274-0.08830.05190.06450.01760.08670.06570.103591.651126.0019-44.0998
217.94092.58960.147711.9846-1.5097.5524-0.2122-0.57390.71230.6537-0.10880.39540.019-0.10440.3210.34210.0875-0.0580.1582-0.07330.278336.706919.83166.168
222.4043-0.0515-0.59645.86731.54242.247-0.07860.10940.0196-0.1065-0.0436-0.3034-0.1307-0.02560.12220.23430.0401-0.07110.10030.02550.137543.66949.520857.8582
232.1134-1.64330.20014.50171.16713.22130.0255-0.10030.01370.21420.0546-0.3965-0.01770.1941-0.08010.1104-0.0485-0.01230.07540.0430.170253.3147-8.225348.219
244.39561.93952.74686.50472.94883.82660.24440.318-0.21510.6878-0.36350.00170.4876-0.15340.11910.2308-0.02050.06930.1530.03430.155745.9211-32.398640.8309
257.05240.96783.54953.81132.13346.03320.3543-0.5541-0.17190.87-0.3918-0.02160.6414-0.75890.03740.3943-0.00690.07980.14030.04730.165545.3347-32.881343.9307
261.81383.61750.458911.5468-1.17784.6824-0.24860.39590.3861-0.47340.149-0.4467-0.37360.13030.09960.19120.0010.02380.19170.10150.233869.94451.89634.4475
274.8743-0.8173-0.17428.5591-3.30482.8951-0.0824-0.280.16540.64370.03870.1672-0.1597-0.01810.04370.13860.01650.01680.1203-0.00640.1663.545142.163314.7005
283.05871.26540.27232.9257-0.66792.17120.0573-0.16670.2235-0.1564-0.0130.0799-0.0592-0.1307-0.04430.040.02260.01670.0914-0.00340.128552.759225.560119.7046
295.1716-1.32052.65894.435-2.54444.3749-0.01380.1797-0.5088-0.25710.0076-0.10460.32890.14450.00620.123-0.05420.030.0507-0.02510.167256.16650.506226.2097
3016.3581-7.066811.986512.4947-10.980412.90050.90261.6905-0.01360.0015-0.8669-0.1793-0.04181.6061-0.03570.1464-0.00620.14050.1560.02610.096261.98164.316225.8097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 89
2X-RAY DIFFRACTION2A90 - 144
3X-RAY DIFFRACTION3A145 - 275
4X-RAY DIFFRACTION4A276 - 294
5X-RAY DIFFRACTION5A295 - 320
6X-RAY DIFFRACTION6B36 - 84
7X-RAY DIFFRACTION7B85 - 138
8X-RAY DIFFRACTION8B139 - 236
9X-RAY DIFFRACTION9B237 - 275
10X-RAY DIFFRACTION10B276 - 320
11X-RAY DIFFRACTION11C37 - 76
12X-RAY DIFFRACTION12C77 - 138
13X-RAY DIFFRACTION13C139 - 193
14X-RAY DIFFRACTION14C194 - 276
15X-RAY DIFFRACTION15C277 - 318
16X-RAY DIFFRACTION16D37 - 68
17X-RAY DIFFRACTION17D69 - 141
18X-RAY DIFFRACTION18D142 - 228
19X-RAY DIFFRACTION19D229 - 276
20X-RAY DIFFRACTION20D277 - 320
21X-RAY DIFFRACTION21E37 - 69
22X-RAY DIFFRACTION22E70 - 138
23X-RAY DIFFRACTION23E139 - 235
24X-RAY DIFFRACTION24E236 - 278
25X-RAY DIFFRACTION25E279 - 320
26X-RAY DIFFRACTION26F37 - 89
27X-RAY DIFFRACTION27F90 - 141
28X-RAY DIFFRACTION28F142 - 240
29X-RAY DIFFRACTION29F241 - 310
30X-RAY DIFFRACTION30F311 - 320

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