[English] 日本語
Yorodumi
- PDB-7mj1: LarB, a carboxylase/hydrolase involved in synthesis of the cofact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mj1
TitleLarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with NAD
ComponentsPyridinium-3,5-biscarboxylic acid mononucleotide synthase
KeywordsLYASE (CARBON-CARBON) / Carboxylase / Hydrolase
Function / homology
Function and homology information


pyridinium-3,5-biscarboxylic acid mononucleotide synthase / 'de novo' IMP biosynthetic process / transferase activity / hydrolase activity / plasma membrane
Similarity search - Function
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase / PurE domain / AIR carboxylase / AIR carboxylase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.402 Å
AuthorsChatterjee, S. / Rankin, J.A. / Lagishetty, S. / Hu, J. / Hausinger, R.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1807073 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128959 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis.
Authors: Rankin, J.A. / Chatterjee, S. / Tariq, Z. / Lagishetty, S. / Desguin, B. / Hu, J. / Hausinger, R.P.
History
DepositionApr 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,48712
Polymers159,0616
Non-polymers1,4266
Water00
1
A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,17912
Polymers212,0828
Non-polymers974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area19720 Å2
ΔGint-206 kcal/mol
Surface area56930 Å2
MethodPISA
2
C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,93020
Polymers212,0828
Non-polymers2,84812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area25530 Å2
ΔGint-282 kcal/mol
Surface area56280 Å2
MethodPISA
3
E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,84116
Polymers212,0828
Non-polymers2,7598
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area26580 Å2
ΔGint-259 kcal/mol
Surface area55780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.445, 120.445, 213.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase / P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB ...P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB / Lactate racemase maturation protein LarB / Lactate racemization operon protein LarB / Nickel-pincer cofactor biosynthesis protein LarB / Nicotinic acid adenine dinucleotide carboxylase/hydrolase / NaAD carboxylase/hydrolase


Mass: 26510.227 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larB, lp_0105 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F9UST0, pyridinium-3,5-biscarboxylic acid mononucleotide synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM magnesium formate, 20% w/v PEG 3350, 2 mM nitrilotriacetic acid neutralized to a pH of ~7.5 with sodium hydroxide, and 0.7 mM zinc sulfate, 10 mM EDTA, 10 mM NAD+ (disodium salt)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.305 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 3.4→41.762 Å / Num. obs: 20627 / % possible obs: 93.8 % / Redundancy: 4.5 % / CC1/2: 0.992 / Net I/σ(I): 7.6
Reflection shellResolution: 3.4→3.67 Å / Num. unique obs: 3997 / CC1/2: 0.674

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D7A

1d7a


Resolution: 3.402→41.762 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 983 4.78 %
Rwork0.2432 19568 -
obs0.2444 20551 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 306.51 Å2 / Biso mean: 110.678 Å2 / Biso min: 36.82 Å2
Refinement stepCycle: final / Resolution: 3.402→41.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8226 0 92 0 8318
Biso mean--116.7 --
Num. residues----1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088479
X-RAY DIFFRACTIONf_angle_d0.87711666
X-RAY DIFFRACTIONf_dihedral_angle_d15.3562747
X-RAY DIFFRACTIONf_chiral_restr0.0511511
X-RAY DIFFRACTIONf_plane_restr0.0061491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4023-3.58160.34191410.3176251885
3.5816-3.80580.35211440.3134281495
3.8058-4.09950.30441370.2691273292
4.0995-4.51160.26371360.2324285495
4.5116-5.16340.23291680.2039284895
5.1634-6.50130.26931320.2715286093
6.5013-41.7620.23611250.2142294290
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)
13.12230.22783.34159.9775-0.99719.01590.714-1.67521.2239-0.6115-0.77551.0710.06772.5649-0.24721.27060.02040.7240.7665-0.41171.442445.8762-22.55422.9188
23.428-4.4698-1.14138.81154.47063.3346-1.74141.6189-1.5536-2.44330.9618-0.12272.26171.970.80552.0267-0.09030.54991.6224-0.40341.132244.3443-23.3193-2.2565
33.11051.0511-1.94362.0938-0.31091.2809-0.97611.2117-1.2152-1.795-0.1444-0.10930.9679-0.81570.36082.9957-0.76961.42491.5726-0.79771.389144.0691-18.7903-11.9789
44.683-0.5429-2.33731.6241-0.07951.6544-1.09970.989-1.5161-1.8045-0.8439-0.73030.9335-0.89610.34242.6177-0.6040.88131.54840.09540.279438.4711-14.7414-3.8248
53.0352-1.2193-4.61371.38451.89418.9927-0.7481.786-0.4622-1.504-0.44041.11840.6086-1.811.07710.8641-0.0291-0.16871.1593-0.23050.772732.2673-11.8197.1338
63.3542-0.3588-0.53472.43930.05877.5901-0.06530.00920.4639-0.995-0.00171.0287-0.7962-0.35610.1540.44970.0704-0.0960.637-0.06760.629529.606-3.24815.2863
78.49610.3549-0.82359.9931-0.53169.669-0.19520.48670.76870.5433-0.007-0.6187-0.0387-0.08090.19610.28620.1239-0.12160.5521-0.02050.545740.8697-7.762817.6491
86.9601-0.8586-0.30735.11552.44015.5421-0.65211.5396-0.40740.1574-0.27831.3790.0535-0.6304-0.96050.99240.5676-1.24091.4561-0.26171.7901-4.0532-31.433322.6098
94.8261-0.1001-1.82963.39782.08521.95970.90061.89010.6146-3.3611-0.383-0.46341.7625-0.6722-0.32651.92080.5796-0.47911.5972-0.22720.74323.5972-37.049916.8506
106.3565-0.24743.56356.81542.74378.1220.31830.53990.2095-1.2005-0.7522-0.6275-0.09010.40040.42550.55080.10630.14460.62440.1490.528219.4715-37.612133.9514
115.08192.9368-2.14162.7676-1.47986.9691-0.1481-0.5163-0.36140.3067-0.1550.09810.195-0.52430.2070.29770.06230.03510.73870.0840.51710.9017-42.42540.0297
123.1729-2.8659-1.75872.692.38418.32171.205-1.4103-0.911-0.80591.1366-0.20480.887-0.15881.13141.5349-0.3238-1.23151.90841.06970.581220.5345-40.371167.002
133.2079-0.06611.32683.424-0.88880.75880.4545-1.51620.56851.6172-0.5442-1.62580.2261-1.3653-0.08491.1588-0.680.06391.61760.01141.478320.7287-34.487367.8462
141.78390.4733-1.67181.995-0.29161.57590.0708-2.2337-0.22711.3698-0.2928-0.21390.20810.38690.0861.9015-0.95930.2373.2154-0.1456-0.147511.5818-35.980173.9399
156.19094.26053.8945.59490.96143.58861.78940.47220.30240.745-1.21250.3335-1.35670.7457-0.86490.9614-0.24120.32861.833-0.71851.09857.3339-24.645357.9035
169.16187.8833.87126.76743.35051.64010.28081.03761.0630.32560.25480.73680.14360.9849-0.290.6936-0.12570.06612.1735-0.22051.254.1872-34.336861.1106
171.5427-2.26162.76973.5727-3.46776.12980.5957-0.8596-0.72450.48370.09630.2699-1.0063-0.2335-0.06610.4372-0.2420.15631.1683-0.67291.2122-1.0375-29.046756.4327
182.6324-0.03051.45342.66382.08752.44140.1039-1.63791.2938-0.6658-0.64241.9351-0.3089-0.73760.5740.59470.1403-0.03630.6123-0.44321.3094-5.4038-30.352649.5757
197.42270.9303-1.07625.07350.59637.9853-0.1452-0.1105-0.21120.2921-0.3197-0.14760.44210.65810.39860.26420.0366-0.01180.5573-0.09890.69123.0499-39.03847.9627
208.9856-3.6639-0.55723.77383.12583.64340.02821.7384-0.09110.1060.2757-0.68920.8007-0.5753-0.19691.7448-0.0170.22331.21570.04230.999266.3311-28.55376.9213
213.64683.5481-5.7143.4105-5.51738.975-0.91040.495-1.059-3.37530.2258-0.19461.95030.02740.43251.56490.1760.52760.76250.01611.064361.4901-28.635370.9749
228.2852-4.0795-4.91444.11153.39888.55690.71050.9912-0.0042-1.2762-0.9520.00420.4293-0.55830.48271.26970.08390.05710.7868-0.04720.681449.9246-25.266871.1655
238.79451.5371.37792.6933-2.85067.78320.11250.1016-0.0306-0.7282-0.77241.18621.5212-2.11010.64511.1808-0.32770.2241.2004-0.30370.79538.4409-19.796782.6393
242.6539-0.2622-0.16849.4040.14948.538-0.897-0.59510.1282-0.89430.3287-1.37640.8768-0.22210.57240.739-0.17170.22430.7295-0.16210.88346.4442-16.197490.236
258.06765.106-0.68556.69982.85054.46961.0340.3601-1.57941.7857-0.0793-1.60491.5583-0.0082-0.95121.65280.314-0.22621.5285-0.76651.708940.019322.0466112.8802
265.75922.0328-0.37018.95660.64323.1968-0.1002-1.65340.2414.60180.2637-0.96430.11771.3836-0.13351.80310.3514-0.29811.8554-0.51271.119237.01217.9288121.4259
275.11221.78972.86832.81424.10038.0024-0.22140.3303-0.23781.7018-0.68850.98170.1002-1.88980.82810.89280.18570.22971.3716-0.19870.879129.61412.1603104.4962
288.0956-4.2813-0.85612.67460.95727.03580.2557-0.97240.4114-1.0745-0.2169-0.7615-1.1032-1.23860.09370.92350.1931-0.00010.84-0.17560.787639.4325.261598.7902
290.1485-0.44680.46042.1112-1.63561.41460.86540.11730.3845-0.72840.0173-0.4038-0.85880.4718-1.02531.32110.05850.30411.1711-0.67391.399631.5174-3.862343.6647
306.2953-0.4491-1.1864.8228-2.15237.8652-0.3417-1.93541.77772.0196-0.85410.7731-1.8894-0.8359-0.41670.73130.57150.35451.0722-0.95711.709832.4096-8.158547.8771
314.03653.73720.00869.29321.29863.54440.111-1.53031.13491.51290.04191.441-0.2872-0.40510.39931.32790.2665-0.12971.5219-0.03970.338736.3724-12.402151.6434
322.58960.4876-3.11038.06753.1285.8674-0.9092-0.10590.33570.72660.03321.6540.6440.04480.93970.7878-0.01310.27540.38020.09630.818333.1722-23.378135.8922
338.89520.5963-2.14367.41853.29415.4855-0.1471-1.3659-1.25511.3941-0.3148-0.19180.58780.54980.47330.6180.0850.05860.68450.25740.721842.3227-21.87436.83
342.73030.2364-3.38446.34024.51387.8326-0.9884-0.8807-2.88031.27060.6065-1.63650.85641.2310.38810.7559-0.13540.53150.70680.03022.072346.6942-33.483827.8662
359.11366.39017.44855.96846.8877.92480.0097-0.5521-1.86861.14510.4688-1.3476-0.65750.4175-0.0970.5890.04970.03670.32180.18310.740344.9505-21.886128.7628
366.1062-1.6566-2.31134.0479-2.75146.27361.0088-0.2680.0645-1.2081-0.9797-1.13670.50410.9552-0.14080.7910.11030.25650.39920.13060.703948.8058-19.898125.9657
372.9721-2.1581.02115.5085-6.94362.00290.2403-1.2149-0.45870.5427-0.24010.51940.7372-0.51050.11880.5352-0.02560.06230.6955-0.03650.518153.6185-11.548324.479
388.04931.17811.63076.93250.97796.37940.1374-0.3751-0.5867-0.2382-0.3030.08760.0779-0.75160.12760.523-0.06520.05090.3978-0.08940.488438.0045-14.714427.2061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 60 )A46 - 60
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 84 )A61 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 94 )A85 - 94
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 107 )A95 - 107
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 141 )A108 - 141
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 190 )A142 - 190
7X-RAY DIFFRACTION7chain 'A' and (resid 191 through 246 )A191 - 246
8X-RAY DIFFRACTION8chain 'C' and (resid 46 through 75 )C46 - 75
9X-RAY DIFFRACTION9chain 'C' and (resid 76 through 107 )C76 - 107
10X-RAY DIFFRACTION10chain 'C' and (resid 108 through 190 )C108 - 190
11X-RAY DIFFRACTION11chain 'C' and (resid 191 through 246 )C191 - 246
12X-RAY DIFFRACTION12chain 'D' and (resid 46 through 66 )D46 - 66
13X-RAY DIFFRACTION13chain 'D' and (resid 67 through 82 )D67 - 82
14X-RAY DIFFRACTION14chain 'D' and (resid 83 through 107 )D83 - 107
15X-RAY DIFFRACTION15chain 'D' and (resid 108 through 125 )D108 - 125
16X-RAY DIFFRACTION16chain 'D' and (resid 126 through 141 )D126 - 141
17X-RAY DIFFRACTION17chain 'D' and (resid 142 through 156 )D142 - 156
18X-RAY DIFFRACTION18chain 'D' and (resid 157 through 188 )D157 - 188
19X-RAY DIFFRACTION19chain 'D' and (resid 189 through 246 )D189 - 246
20X-RAY DIFFRACTION20chain 'E' and (resid 36 through 58 )E36 - 58
21X-RAY DIFFRACTION21chain 'E' and (resid 59 through 82 )E59 - 82
22X-RAY DIFFRACTION22chain 'E' and (resid 83 through 125 )E83 - 125
23X-RAY DIFFRACTION23chain 'E' and (resid 126 through 177 )E126 - 177
24X-RAY DIFFRACTION24chain 'E' and (resid 178 through 246 )E178 - 246
25X-RAY DIFFRACTION25chain 'F' and (resid 44 through 60 )F44 - 60
26X-RAY DIFFRACTION26chain 'F' and (resid 61 through 106 )F61 - 106
27X-RAY DIFFRACTION27chain 'F' and (resid 107 through 190 )F107 - 190
28X-RAY DIFFRACTION28chain 'F' and (resid 191 through 246 )F191 - 246
29X-RAY DIFFRACTION29chain 'B' and (resid 44 through 66 )B44 - 66
30X-RAY DIFFRACTION30chain 'B' and (resid 67 through 87 )B67 - 87
31X-RAY DIFFRACTION31chain 'B' and (resid 88 through 107 )B88 - 107
32X-RAY DIFFRACTION32chain 'B' and (resid 108 through 125 )B108 - 125
33X-RAY DIFFRACTION33chain 'B' and (resid 126 through 156 )B126 - 156
34X-RAY DIFFRACTION34chain 'B' and (resid 157 through 168 )B157 - 168
35X-RAY DIFFRACTION35chain 'B' and (resid 169 through 180 )B169 - 180
36X-RAY DIFFRACTION36chain 'B' and (resid 181 through 207 )B181 - 207
37X-RAY DIFFRACTION37chain 'B' and (resid 208 through 220 )B208 - 220
38X-RAY DIFFRACTION38chain 'B' and (resid 221 through 246 )B221 - 246

+
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