[English] 日本語
Yorodumi
- PDB-5mcp: Structure of IMP dehydrogenase from Ashbya gossypii bound to ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mcp
TitleStructure of IMP dehydrogenase from Ashbya gossypii bound to ATP
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMP dehydrogenase / Ashbya gossypii / allosteric modulator / purine nucleotides
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesAshbya gossypii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWinter, G. / Fernandez-Justel, D. / de Pereda, J.M. / Revuelta, J.L. / Buey, R.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-79237-P Spain
CitationJournal: Sci Rep / Year: 2017
Title: A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases.
Authors: Buey, R.M. / Fernandez-Justel, D. / Marcos-Alcalde, I. / Winter, G. / Gomez-Puertas, P. / de Pereda, J.M. / Luis Revuelta, J.
History
DepositionNov 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conf
Item: _pdbx_audit_support.funding_organization / _struct_conf.beg_auth_comp_id ..._pdbx_audit_support.funding_organization / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 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
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,68340
Polymers453,3178
Non-polymers12,36732
Water22,9871276
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44050 Å2
ΔGint-296 kcal/mol
Surface area136930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.891, 152.090, 152.255
Angle α, β, γ (deg.)90.00, 93.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Inosine-5'-monophosphate dehydrogenase / IMPDH


Mass: 56664.574 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus)
Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: AGOS_AER117W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q756Z6, IMP dehydrogenase
#2: Chemical...
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1276 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Imidazole + 0.05 M Mes; pH 6.5 20 % Glycerol 20 % PEG-4000 0.02 M D-glucose 0.02 M D-Mannose 0.02 M D_Galactose 0.02 M L-Fucose 0.02 M C-Xylose 0.02 M N-Acetyl-D-Glucosamine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.4→152.042 Å / Num. obs: 226714 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.206 / Net I/σ(I): 5.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.487 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.686 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z0G

4z0g


Resolution: 2.4→152.042 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 11355 5.02 %
Rwork0.2494 --
obs0.2505 226233 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→152.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22478 0 752 1276 24506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323593
X-RAY DIFFRACTIONf_angle_d0.58832138
X-RAY DIFFRACTIONf_dihedral_angle_d12.73913743
X-RAY DIFFRACTIONf_chiral_restr0.0433799
X-RAY DIFFRACTIONf_plane_restr0.0044078
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.24880.7623-0.54970.961-0.88681.13210.07760.0688-0.07220.11390.12640.1183-0.0241-0.33840.02990.236-0.0162-0.01390.25380.05950.1723-6.1652-36.309-22.8315
21.48290.5691-0.75981.8592-0.14620.3142-0.19080.1717-0.2789-0.25260.12180.16350.0349-0.2662-0.00750.5713-0.0922-0.02410.38740.08140.3354-11.1208-49.9645-17.1644
31.0760.6758-0.33911.5378-0.00991.81810.06720.0280.01650.06030.05070.04640.0167-0.1114-0.0010.40140.0264-0.01110.20140.04570.16776.5886-24.5058-21.0567
41.2257-0.7830.61913.1021-0.55891.44890.06130.1279-0.0731-0.0203-0.1276-0.5642-0.05810.21870.08660.35950.02620.04290.24980.01020.227721.5731-11.4018-20.5173
51.269-0.6017-0.61490.66740.74270.95780.0732-0.0329-0.0606-0.0777-0.26220.368-0.0005-0.2782-0.00750.4267-0.01830.0070.3152-0.11370.3519-14.148819.86940.1078
61.0659-0.6616-0.69020.55650.48791.2487-0.0369-0.1905-0.07510.1123-0.00310.32410.1319-0.16150.03660.5753-0.05950.07230.3954-0.05390.324-12.526120.20289.2904
70.9687-0.3345-0.67622.2328-0.11181.41420.0563-0.0204-0.05020.0319-0.09630.1625-0.0571-0.053-0.00950.4239-0.0021-0.03270.2217-0.04280.16726.166115.0518-14.8665
81.3230.48210.55311.2610.52043.21010.031-0.0129-0.0498-0.02570.153-0.23940.37290.6859-0.10350.4050.0465-0.01440.243-0.02890.191121.923414.8037-27.3715
91.4292-0.91880.42731.0903-1.48390.73940.0467-0.01250.08750.12630.23420.29730.1037-0.515-0.00640.44780.04470.03260.43280.10370.3089-11.639437.4109-60.4723
101.1437-0.4350.92111.0772-0.49310.7136-0.2139-0.1840.25850.37650.12250.1449-0.1435-0.3478-0.01910.63370.06510.04140.42230.04480.3661-8.99646.4205-60.3576
111.2022-0.74860.17931.57540.13952.29670.0413-0.0380.0127-0.04760.05560.03580.0277-0.10550.01080.4026-0.03430.00790.17450.05640.15568.202521.2731-54.3424
120.960.72830.68561.88091.05450.8472-0.01550.00680.0303-0.2098-0.11010.17330.0163-0.0324-0.01630.40460.0076-0.00380.22-0.0010.18635.6171-12.4897-66.2322
131.47760.51250.83441.54580.30731.2903-0.05380.12840.1651-0.0642-0.0950.7727-0.1216-0.3628-0.01550.47060.0723-0.09510.4274-0.12120.575-16.9307-26.1436-87.9998
140.93540.41710.66321.79340.24721.56040.05460.04330.0607-0.0001-0.11080.1228-0.0047-0.0363-0.00770.38220.00680.03120.2078-0.04580.17028.5814-18.2379-60.5974
150.9756-0.3075-0.56420.61910.20370.38070.1173-0.0753-0.27460.3323-0.68240.15990.2037-0.6941-0.06070.8222-0.1113-0.00620.9878-0.12861.083-89.278-14.9284-24.0037
160.4102-0.81560.68622.3429-0.41252.2082-0.1092-0.46540.63530.79670.44110.0920.0879-0.2653-0.06980.44780.0384-0.14770.81460.12991.2421-76.2065-19.0223-34.4269
170.2215-0.08180.43180.58820.00610.94920.484-0.32970.06140.21220.0658-0.09310.56770.2558-0.00780.83280.1595-0.22650.9399-0.03521.261-64.9286-38.8929-41.1152
180.99740.6101-0.62581.2719-0.74232.101-0.14150.4111-0.2977-0.12090.2414-0.65580.1692-0.1021-0.06660.51510.2434-0.16941.019-0.03761.4317-56.9711-43.6527-53.1675
190.268-0.17190.1540.14580.13030.60180.54040.1775-0.8704-0.4695-0.34310.4563-0.6660.19020.00480.863-0.0255-0.32231.2643-0.03760.9812-41.122-59.3999-35.7835
201.2665-0.13520.18731.0684-0.21360.62090.1450.13240.27640.2953-0.1355-0.76420.27620.3755-0.04790.82380.0856-0.17851.03360.021.2423-72.6073-36.4534-54.1227
211.424-0.4112-0.65490.12510.11540.35960.05110.013-0.04330.30990.13970.1116-0.1241-0.1226-0.05040.75370.1488-0.16710.99140.10260.9727-62.6838-30.0229-40.2074
220.749-0.71660.04870.6759-0.04730.52440.2897-0.315-0.44410.8488-0.15120.30220.4953-0.4357-0.01010.84920.113-0.23250.75380.0131.23-73.8631-28.7039-30.9804
230.00370.08160.07850.9510.70130.93380.4287-0.38990.336-0.1601-0.150.6705-0.836-0.6983-0.09330.67970.16940.26240.82970.3491.4224-89.123215.9955-32.7
240.10150.38850.13371.02130.17270.62250.6238-0.4590.09580.06680.5771-0.9405-0.15360.57120.04630.8559-0.11680.17941.0991-0.01861.3323-76.98124.1967-20.1231
250.5594-0.2346-0.39940.07930.16290.31360.40460.5988-0.07440.0102-0.09180.26960.2446-0.66130.22570.6569-0.4021-0.30780.87240.13421.6536-52.6282-6.25972.6979
260.5710.9866-0.05031.7199-0.44662.3654-0.2942-0.74450.20750.39930.17810.39830.40760.38650.01291.0784-0.11720.03310.84380.15561.2891-33.50732.921520.3797
270.26520.13370.06220.0880.04370.11420.0633-0.23640.2715-0.12650.0414-0.0418-0.1404-0.01880.20080.7527-0.70740.66991.1384-0.12462.0222-55.7312.077812.3308
280.4368-0.0451-0.11210.1651-0.19940.33070.0695-0.22730.08270.16540.26060.1209-0.2510.5664-0.0670.5696-0.0488-0.23061.061-0.04661.1629-73.8484-17.5901-6.5517
291.5212-0.15070.85311.4907-0.20741.69360.048-0.17650.40240.37310.1061-0.3651-0.4630.2740.0220.8531-0.085-0.09150.8309-0.09981.4654-78.8794-9.7268-19.6901
300.6390.7648-0.26261.11720.09770.93180.63910.31880.70750.2332-0.32990.5872-0.94810.1010.08020.7207-0.3340.1871.0091-0.05371.5083-74.31494.9277-18.2223
310.97750.0175-0.04220.7184-0.00850.6618-0.01410.27680.091-0.4828-0.0816-0.17870.29390.3275-0.04050.69230.13580.13061.05440.22731.1499-72.2321-10.6943-67.8443
320.9225-0.0556-0.22960.15830.21730.26250.65370.45340.30150.2001-0.1372-0.4865-0.1421-0.7124-0.0390.98620.1947-0.08230.99120.18771.7608-37.8876-3.9335-97.0247
331.0607-1.1079-0.47611.09580.54650.16330.07220.03580.26271.00150.03420.0612-0.0448-0.1395-0.08280.85760.16730.25231.01440.21881.528-65.15956.6798-84.9764
340.66490.2514-0.34020.9482-0.11620.83690.50540.08320.2201-0.361-0.2458-0.1123-0.59060.0686-0.03950.98220.04320.09161.03560.07441.167-71.4431-5.2811-69.0156
350.6123-0.3659-0.01780.58270.12560.3276-0.19060.28780.2773-0.2124-0.4397-0.2045-0.3484-0.19790.09940.47290.09640.2231.15650.18481.5011-84.38588.6177-60.6875
360.5191-0.01570.20140.5172-0.21730.232-0.17240.30940.8184-0.15370.1036-0.3425-0.3909-0.7769-0.03681.0352-0.0790.41910.98080.00831.5033-69.452328.4925-47.7212
370.0277-0.1675-0.02371.03560.1130.0436-0.104-0.3921-0.29530.0506-0.44351.10520.05160.0886-0.27030.8285-0.19340.45471.1044-0.00421.217-51.035643.3436-37.6332
380.66-0.4249-0.85271.76110.33731.25690.3473-0.36370.74590.35710.06310.28410.1167-0.2318-0.04981.09220.02720.19621.5698-0.13560.8123-31.207556.2501-43.1162
391.0538-0.08172.0260.3364-0.04943.9421-0.54690.08810.72420.066-0.4249-0.033-0.1889-0.151-0.41980.66610.39940.42541.34590.12551.4438-44.426857.4543-52.8747
401.14990.2778-0.1860.1492-0.6854.62840.3265-0.41751.16840.0011-0.0214-0.1906-0.3658-0.291-0.11190.8241-0.05030.39510.5488-0.09191.8997-66.06743.1278-38.0759
410.7052-0.25520.25390.8139-0.03660.71920.6920.03260.2116-0.2302-0.2085-0.2023-0.2482-0.0435-0.06111.0595-0.09570.39820.7509-0.00471.4798-75.058825.5631-38.8732
421.2009-1.11560.49521.26330.15721.7568-0.02940.5798-0.23790.1855-0.02160.65860.68670.55970.18720.62470.21140.41620.8260.07141.7419-80.82219.8826-54.9608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 195 )
2X-RAY DIFFRACTION2chain 'A' and (resid 196 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 507 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 37 )
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 195 )
6X-RAY DIFFRACTION6chain 'B' and (resid 196 through 256 )
7X-RAY DIFFRACTION7chain 'B' and (resid 257 through 507 )
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 37 )
9X-RAY DIFFRACTION9chain 'C' and (resid 38 through 195 )
10X-RAY DIFFRACTION10chain 'C' and (resid 196 through 256 )
11X-RAY DIFFRACTION11chain 'C' and (resid 257 through 507 )
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 132 )
13X-RAY DIFFRACTION13chain 'D' and (resid 133 through 256 )
14X-RAY DIFFRACTION14chain 'D' and (resid 257 through 507 )
15X-RAY DIFFRACTION15chain 'E' and (resid 4 through 27 )
16X-RAY DIFFRACTION16chain 'E' and (resid 28 through 51 )
17X-RAY DIFFRACTION17chain 'E' and (resid 52 through 90 )
18X-RAY DIFFRACTION18chain 'E' and (resid 91 through 113 )
19X-RAY DIFFRACTION19chain 'E' and (resid 114 through 238 )
20X-RAY DIFFRACTION20chain 'E' and (resid 239 through 372 )
21X-RAY DIFFRACTION21chain 'E' and (resid 373 through 459 )
22X-RAY DIFFRACTION22chain 'E' and (resid 460 through 499 )
23X-RAY DIFFRACTION23chain 'F' and (resid 4 through 27 )
24X-RAY DIFFRACTION24chain 'F' and (resid 28 through 67 )
25X-RAY DIFFRACTION25chain 'F' and (resid 69 through 165 )
26X-RAY DIFFRACTION26chain 'F' and (resid 166 through 196 )
27X-RAY DIFFRACTION27chain 'F' and (resid 197 through 238 )
28X-RAY DIFFRACTION28chain 'F' and (resid 239 through 319 )
29X-RAY DIFFRACTION29chain 'F' and (resid 320 through 360 )
30X-RAY DIFFRACTION30chain 'F' and (resid 361 through 499 )
31X-RAY DIFFRACTION31chain 'G' and (resid 3 through 102 )
32X-RAY DIFFRACTION32chain 'G' and (resid 103 through 206 )
33X-RAY DIFFRACTION33chain 'G' and (resid 207 through 309 )
34X-RAY DIFFRACTION34chain 'G' and (resid 310 through 501 )
35X-RAY DIFFRACTION35chain 'H' and (resid 3 through 40 )
36X-RAY DIFFRACTION36chain 'H' and (resid 41 through 81 )
37X-RAY DIFFRACTION37chain 'H' and (resid 82 through 142 )
38X-RAY DIFFRACTION38chain 'H' and (resid 143 through 184 )
39X-RAY DIFFRACTION39chain 'H' and (resid 185 through 228 )
40X-RAY DIFFRACTION40chain 'H' and (resid 234 through 268 )
41X-RAY DIFFRACTION41chain 'H' and (resid 269 through 478 )
42X-RAY DIFFRACTION42chain 'H' and (resid 479 through 499 )

+
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