[English] 日本語
Yorodumi
- PDB-8ur2: Crystal Structure of macrophage migration inhibitory factor (MIF)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ur2
TitleCrystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (I41 form)
ComponentsMACROPHAGE MIGRATION INHIBITORY FACTOR
KeywordsCYTOKINE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / macrophage migration inhibitory factor
Function / homology
Function and homology information


phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine activity / extracellular space
Similarity search - Function
Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
IODIDE ION / PYRUVIC ACID / L-dopachrome isomerase
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Structures of Trichomonas vaginalis macrophage migratory inhibitory factor.
Authors: Srivastava, A. / Nair, A. / Dawson, O.C.O. / Gao, R. / Liu, L. / Craig, J.K. / Battaile, K.P. / Harmon, E.K. / Barrett, L.K. / Van Voorhis, W.C. / Subramanian, S. / Myler, P.J. / Lovell, S. ...Authors: Srivastava, A. / Nair, A. / Dawson, O.C.O. / Gao, R. / Liu, L. / Craig, J.K. / Battaile, K.P. / Harmon, E.K. / Barrett, L.K. / Van Voorhis, W.C. / Subramanian, S. / Myler, P.J. / Lovell, S. / Asojo, O.A. / Darwiche, R.
History
DepositionOct 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Revision 2.1Dec 11, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MACROPHAGE MIGRATION INHIBITORY FACTOR
B: MACROPHAGE MIGRATION INHIBITORY FACTOR
C: MACROPHAGE MIGRATION INHIBITORY FACTOR
D: MACROPHAGE MIGRATION INHIBITORY FACTOR
E: MACROPHAGE MIGRATION INHIBITORY FACTOR
F: MACROPHAGE MIGRATION INHIBITORY FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2728
Polymers89,0576
Non-polymers2152
Water3,009167
1
A: MACROPHAGE MIGRATION INHIBITORY FACTOR
B: MACROPHAGE MIGRATION INHIBITORY FACTOR
C: MACROPHAGE MIGRATION INHIBITORY FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7435
Polymers44,5283
Non-polymers2152
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-27 kcal/mol
Surface area12920 Å2
MethodPISA
2
D: MACROPHAGE MIGRATION INHIBITORY FACTOR
E: MACROPHAGE MIGRATION INHIBITORY FACTOR
F: MACROPHAGE MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)44,5283
Polymers44,5283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-27 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.390, 118.390, 106.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11B-201-

IOD

-
Components

#1: Protein
MACROPHAGE MIGRATION INHIBITORY FACTOR


Mass: 14842.798 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_219770 / Plasmid: TrvaA.00834.a.UX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2DXT4
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. 5 mM sodium ...Details: Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. 5 mM sodium pyruvate added to the protien prior to crystallization. Plate: 13618 well B12 drop 2, Puck: PSL-0111, Cryo: Direct

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 8, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→83.71 Å / Num. obs: 57827 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Rrim(I) all: 0.078 / Χ2: 1.02 / Net I/σ(I): 16.6 / Num. measured all: 787413
Reflection shellResolution: 1.9→1.95 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 1.619 / Num. measured all: 58149 / Num. unique obs: 4271 / CC1/2: 0.637 / Rpim(I) all: 0.454 / Rrim(I) all: 1.682 / Χ2: 1.06 / Net I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→83.71 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2990 5.18 %
Rwork0.192 --
obs0.1939 57681 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→83.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 7 167 4887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114809
X-RAY DIFFRACTIONf_angle_d0.9096486
X-RAY DIFFRACTIONf_dihedral_angle_d12.0961705
X-RAY DIFFRACTIONf_chiral_restr0.067739
X-RAY DIFFRACTIONf_plane_restr0.007830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.38331450.34072599X-RAY DIFFRACTION100
1.93-1.960.34081270.29432620X-RAY DIFFRACTION100
1.96-20.32061720.262561X-RAY DIFFRACTION100
2-2.040.27951500.24292587X-RAY DIFFRACTION100
2.04-2.080.25951400.23062592X-RAY DIFFRACTION100
2.08-2.130.24211300.22142632X-RAY DIFFRACTION100
2.13-2.170.25351360.20882609X-RAY DIFFRACTION100
2.18-2.230.22091520.20672572X-RAY DIFFRACTION100
2.23-2.290.23831380.20732611X-RAY DIFFRACTION100
2.29-2.360.23921300.21292629X-RAY DIFFRACTION100
2.36-2.430.24221270.21752605X-RAY DIFFRACTION100
2.43-2.520.2911600.20152592X-RAY DIFFRACTION100
2.52-2.620.25591520.21232613X-RAY DIFFRACTION100
2.62-2.740.25811390.19992608X-RAY DIFFRACTION100
2.74-2.880.25441530.21052602X-RAY DIFFRACTION100
2.88-3.070.3071130.22642629X-RAY DIFFRACTION100
3.07-3.30.23521310.19662630X-RAY DIFFRACTION100
3.3-3.630.21611540.18872583X-RAY DIFFRACTION100
3.63-4.160.18541560.16272601X-RAY DIFFRACTION100
4.16-5.240.19491320.1482635X-RAY DIFFRACTION99
5.24-83.710.21571530.18742581X-RAY DIFFRACTION97
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)
17.06192.14890.50956.6446-1.04416.18970.14660.0652-0.02320.2151-0.0299-0.3512-0.07350.5231-0.08180.31370.05270.0710.2827-0.04410.389828.22289.247133.0844
24.63432.65176.03265.15483.07628.9381-0.47590.06771.1044-0.08050.19020.0991-1.08880.87920.10810.3311-0.02330.10230.4026-0.08160.573329.310717.902833.4761
33.76361.96-1.29714.2084-0.75163.9679-0.0411-0.36090.30690.04360.0152-0.1249-0.32330.36160.05780.25730.04790.04740.3341-0.04610.396526.01177.541934.5071
41.81740.09162.65566.8368-0.71017.6483-0.138-1.16350.21140.3279-0.0483-1.15460.58510.91760.13540.41320.1406-0.06180.5779-0.05810.585634.52976.410340.6493
56.9353.55323.1537.48640.23217.27040.2981-1.08740.95180.65970.1528-0.1165-0.11370.9975-0.36030.40340.08730.06150.5841-0.1690.353726.647914.369144.3476
62.4092.41681.0234.44141.20414.0089-0.2003-0.3419-0.58260.52870.15060.25990.31930.57060.02890.5060.12980.07980.43190.0360.377825.78615.802842.3911
79.31384.9695-6.42452.9718-3.44624.49820.537-0.80480.4896-0.04480.4444-0.43810.3431.2205-0.9970.78460.00650.12210.9321-0.18651.034349.71915.293133.9898
83.5235-2.0017-0.79483.7533-0.45086.3253-0.22910.02510.03230.17550.29280.0009-0.0162-0.1231-0.06290.2283-0.03640.01640.33070.0040.396935.8013-0.56722.5503
93.6624-4.50973.0776.0387-4.17043.94490.43460.7055-0.5349-0.6597-0.01180.04270.55750.5411-0.43430.3362-0.00790.05480.4135-0.06950.452441.1716-5.12517.0865
103.5424-1.4939-0.3817.56752.18782.1303-0.0583-0.0821-0.00370.03650.1967-0.13720.15730.253-0.12320.2444-0.00740.04760.32920.01180.307138.72270.555525.9665
114.0425-3.95734.09454.1565-4.06844.0945-0.1855-0.1603-0.11150.06070.21-0.79530.00170.66520.1640.3412-0.03770.04660.5243-0.03730.553649.31581.188523.6176
123.7598-3.06063.18726.6541-4.5446.2457-0.11160.01350.49060.03570.258-0.0875-0.0655-0.2940.02850.2512-0.05320.0260.3318-0.03250.445143.49187.276426.6068
133.4880.42341.56771.4224-1.72447.2674-0.2441-0.13130.02760.1985-0.0138-0.0607-0.5590.12160.26590.32890.04220.00660.23490.00250.413523.2599-5.793230.8018
147.3888-4.63115.75734.3729-4.49565.5796-0.0974-0.4927-0.27570.07630.3390.36-0.1137-1.1513-0.31490.3059-0.04780.06940.31270.04250.421816.4065-10.007135.0127
156.41254.4836-5.7395.2385-5.82976.72780.4329-0.86460.07340.9171-0.4569-0.0953-1.24530.53910.06650.3847-0.00030.03120.442-0.01020.422520.6344-4.98541.1223
162.6676-2.1489-3.39048.3507-0.72667.22330.05470.5847-0.0806-0.7312-0.26910.08410.0536-0.13830.21550.308-0.01920.02730.3283-0.06440.390330.3494-10.22819.3053
177.6196-1.04040.84732.14011.93095.1239-0.1169-1.4679-0.05920.27220.35-0.3945-0.9689-0.07970.04530.32750.0410.03050.55190.10470.455730.3455-9.452938.1186
188.6353-3.67463.75345.5576-0.2912.4235-0.4165-0.4519-0.52470.47540.2366-0.20280.4824-0.16330.13610.4635-0.02850.11130.34570.06270.481824.271-18.371535.1216
197.1847-0.83190.8748.3054-1.00419.5409-0.051-0.1498-0.6369-0.33860.0401-0.60410.46560.566-0.09580.30650.06430.08830.31250.07970.482930.2245-14.614329.8159
206.2422-1.43163.38157.38430.46073.88270.27070.1408-0.2719-0.46-0.0071-0.35450.1025-0.3092-0.24230.26-0.03980.04920.31920.03390.3511.5892-30.80620.6733
218.0579-1.7884-1.07886.29395.10824.3972-0.2413-0.224-0.39710.42850.8071-0.78950.57280.6626-0.4240.45420.06220.06870.33870.10750.41756.5271-38.427824.0077
228.3584-2.63890.23227.5951-0.01594.27630.10580.1329-0.17340.0461-0.01310.09740.3946-0.495-0.04720.3067-0.02760.0090.36010.03590.1971-0.8685-31.25219.5062
232.3396-1.36740.66628.79732.72462.58050.21860.824-0.0123-1.2711-0.28670.7597-0.0993-0.5496-0.04470.5512-0.0914-0.11270.7847-0.13110.5399-0.533-37.386811.0745
248.06921.68852.18056.69694.82853.8476-0.61520.0214-1.3153-0.53710.25650.06170.5365-0.17190.4880.7409-0.23530.17240.50410.04740.7935-3.7866-42.848120.952
256.35240.1808-5.21612.5134-0.81934.4515-0.50890.4606-0.8426-0.4976-0.0641-0.1590.9925-0.07810.68050.6033-0.0690.02680.8112-0.09640.71182.0782-35.76759.34
264.70180.89790.17256.2693-1.35093.92690.05260.3725-0.38740.09510.27360.15650.27650.0423-0.29730.21260.01610.03740.3115-0.05380.30749.0031-20.345710.5292
272.6405-0.7204-2.67033.03370.30192.6950.04520.40310.1982-0.15590.1837-0.1655-0.1979-0.0362-0.2690.3509-0.06120.04790.47190.01420.450512.282-14.45842.8707
281.0554-1.81710.12568.5973-4.67918.9432-0.2204-0.0987-0.0234-0.01990.0281-0.25580.30960.17750.12270.252-0.02680.02940.3332-0.03180.435810.1534-26.300213.4441
298.3813-7.5796-7.48846.84946.78076.73712.28680.6535-1.2375-1.9161-1.41741.06460.8891-2.107-0.85971.0026-0.2864-0.11671.4981-0.08240.55664.8344-26.3616-6.6032
304.55080.9323-1.41867.0467-0.1828.2457-0.29140.2928-0.1865-0.65590.0792-0.30120.45130.19830.21010.35060.00630.09570.376-0.05070.421415.8837-27.45374.884
315.13491.373-1.68232.9329-3.3724.2212-0.15380.82470.27430.07920.30120.2431-0.8063-0.6602-0.08030.25230.1510.0710.50950.03790.4046-5.4087-17.469814.7185
326.3442.02875.29635.6306-0.02965.2205-0.1331.27890.37540.19330.2010.6772-0.5071-1.04190.23280.34870.23940.04561.21230.07110.5619-15.329-17.598916.0565
339.20410.78324.87415.25091.91544.50090.05260.841-1.0077-0.50080.27710.90670.3885-1.6138-0.18590.3938-0.0845-0.03371.07190.05060.633-14.3877-26.163214.3809
343.49620.5776-3.1735.3454-0.11062.97490.48910.58910.37060.51640.10380.1336-1.8478-0.443-0.6460.54790.06770.06990.43680.06260.40713.2488-10.14069.41
353.88393.04275.6577.36624.19518.1540.07180.404-0.09120.23540.0124-0.12960.6858-1.23040.08360.412-0.1390.05161.2855-0.08910.4371-8.1594-23.16345.4799
365.4023-1.57260.23461.8066-0.39382.7243-0.15081.29380.4807-0.35950.15420.3972-0.1169-1.7855-0.82050.01110.5899-0.27511.81970.6420.6395-14.1267-14.07215.3427
378.94110.95462.65286.5792.28216.5323-0.22631.43861.3373-0.41080.48970.1182-0.8363-1.3845-0.07420.51460.18780.05761.10570.23530.3388-5.4941-13.91814.3274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 83 )
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 101 )
6X-RAY DIFFRACTION6chain 'A' and (resid 102 through 115 )
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 13 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 45 )
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 83 )
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 101 )
12X-RAY DIFFRACTION12chain 'B' and (resid 102 through 113 )
13X-RAY DIFFRACTION13chain 'C' and (resid 13 through 26 )
14X-RAY DIFFRACTION14chain 'C' and (resid 27 through 45 )
15X-RAY DIFFRACTION15chain 'C' and (resid 46 through 57 )
16X-RAY DIFFRACTION16chain 'C' and (resid 58 through 71 )
17X-RAY DIFFRACTION17chain 'C' and (resid 72 through 83 )
18X-RAY DIFFRACTION18chain 'C' and (resid 84 through 101 )
19X-RAY DIFFRACTION19chain 'C' and (resid 102 through 114 )
20X-RAY DIFFRACTION20chain 'D' and (resid 14 through 26 )
21X-RAY DIFFRACTION21chain 'D' and (resid 27 through 45 )
22X-RAY DIFFRACTION22chain 'D' and (resid 46 through 71 )
23X-RAY DIFFRACTION23chain 'D' and (resid 72 through 83 )
24X-RAY DIFFRACTION24chain 'D' and (resid 84 through 101 )
25X-RAY DIFFRACTION25chain 'D' and (resid 102 through 128 )
26X-RAY DIFFRACTION26chain 'E' and (resid 13 through 26 )
27X-RAY DIFFRACTION27chain 'E' and (resid 27 through 51 )
28X-RAY DIFFRACTION28chain 'E' and (resid 52 through 77 )
29X-RAY DIFFRACTION29chain 'E' and (resid 78 through 83 )
30X-RAY DIFFRACTION30chain 'E' and (resid 84 through 114 )
31X-RAY DIFFRACTION31chain 'F' and (resid 14 through 26 )
32X-RAY DIFFRACTION32chain 'F' and (resid 27 through 45 )
33X-RAY DIFFRACTION33chain 'F' and (resid 46 through 57 )
34X-RAY DIFFRACTION34chain 'F' and (resid 58 through 71 )
35X-RAY DIFFRACTION35chain 'F' and (resid 72 through 83 )
36X-RAY DIFFRACTION36chain 'F' and (resid 84 through 101 )
37X-RAY DIFFRACTION37chain 'F' and (resid 102 through 113 )

+
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