[English] 日本語
Yorodumi
- PDB-7mj2: LarB, a carboxylase/hydrolase involved in synthesis of the cofact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mj2
TitleLarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with Zn
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
Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
B: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,26511
Polymers159,0616
Non-polymers2045
Water3,009167
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)212,44116
Polymers212,0828
Non-polymers3598
Water1448
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 area20620 Å2
ΔGint-365 kcal/mol
Surface area58820 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)212,53820
Polymers212,0828
Non-polymers45612
Water1448
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 area21920 Å2
ΔGint-407 kcal/mol
Surface area55410 Å2
MethodPISA
3
E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

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

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

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


Theoretical massNumber of molelcules
Total (without water)212,0828
Polymers212,0828
Non-polymers00
Water1448
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 area20060 Å2
ΔGint-175 kcal/mol
Surface area55890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.102, 120.102, 212.575
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.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 75 mM magnesium formate, 2 mM nitrilotriacetic acid (pH to 7.5 with sodium hydroxide), 0.7 mM zinc sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.796→34.03 Å / Num. obs: 39160 / % possible obs: 99.6 % / Redundancy: 22.6 % / CC1/2: 0.999 / Net I/σ(I): 18.5
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 18.9 % / Rmerge(I) obs: 0.088 / Num. unique obs: 4327 / CC1/2: 0.891 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Χ2: 5.877 / % possible all: 99.8

-
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: 2.8→33.981 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1921 4.94 %
Rwork0.2099 36939 -
obs0.2116 38860 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215 Å2 / Biso min: 11.46 Å2
Refinement stepCycle: final / Resolution: 2.8→33.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8615 0 5 167 8787
Biso mean--46.47 36.67 -
Num. residues----1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098750
X-RAY DIFFRACTIONf_angle_d1.00311962
X-RAY DIFFRACTIONf_dihedral_angle_d16.6823014
X-RAY DIFFRACTIONf_chiral_restr0.0651499
X-RAY DIFFRACTIONf_plane_restr0.0071546
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.870.35781550.30982591100
2.87-2.94760.31851170.28782619100
2.9476-3.03430.3021210.26362605100
3.0343-3.13210.26151440.2566255899
3.1321-3.2440.2991360.24642627100
3.244-3.37380.26881490.24072584100
3.3738-3.52720.23161180.21442653100
3.5272-3.71290.26921430.21222608100
3.7129-3.94520.26091370.1992650100
3.9452-4.24930.2291440.1922648100
4.2493-4.67590.18651330.16822659100
4.6759-5.35030.24141480.18222687100
5.3503-6.73220.25361280.2283268898
6.7322-33.9810.19081480.1771276296
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)
19.1756-0.3649-4.03542.01551.6255.9195-0.0676-0.757-0.795-0.2641-0.3317-0.50540.83731.06870.44750.47660.1940.04180.750.05220.273144.1914-22.20774.6686
27.001-4.2121-4.35543.01592.09058.617-0.41170.7797-1.0558-0.5767-0.1416-0.49321.6790.35580.53450.78420.22190.18510.61830.00490.432444.3721-23.1276-2.2749
32.5924-1.6054-1.83211.54411.65695.27880.06781.0888-0.3154-0.8768-0.3976-0.24120.16750.38520.29010.59210.13040.07010.772-0.01820.266441.7272-15.0301-6.9091
43.2057-0.5081-0.33873.28980.38993.6628-0.00210.7991-0.6039-0.5406-0.08610.4940.9342-0.76110.09260.4217-0.1169-0.06390.4601-0.17770.504727.7592-14.30068.2808
54.3548-0.5781-0.57441.52920.08723.5761-0.06480.54030.0913-0.4451-0.20790.6197-0.109-0.46740.20540.20660.0332-0.08220.259-0.06360.349132.8144-8.06417.1624
64.14151.33290.11611.23750.05441.335-0.06040.08770.5881-0.0754-0.05490.5671-0.0885-0.36110.10080.1902-0.0244-0.09850.3102-0.1340.724625.55263.305416.2113
73.4339-1.8340.23063.22081.43755.82250.0884-0.06440.6740.0447-0.21430.1293-0.1055-0.07810.09380.10830.0284-0.0350.1326-0.05280.392935.1647-3.194718.0015
83.6297-0.51561.91844.83271.91662.2844-0.1378-0.10080.39120.2560.0064-0.339-0.43970.590.10740.2521-0.0694-0.07270.2602-0.050.475345.8069-0.593221.2126
92.7663-0.93690.27931.50060.43523.7893-0.09350.1647-0.26490.18170.03920.10660.5458-0.2471-0.00310.1788-0.0750.02640.14-0.04030.326137.4977-14.528416.1167
101.6337-0.8469-0.81892.1779-1.22571.977-0.13540.09180.6541-0.08110.06720.0458-0.56380.24960.07770.5384-0.023-0.09050.89390.0580.661513.0079-34.33679.9316
111.17760.80151.84555.10961.81313.052-0.25-1.29750.59440.8190.25040.301-0.48330.38190.10250.5902-0.0660.08280.9021-0.29630.457732.0144-8.792747.1328
123.9311-0.9228-1.41753.650.42133.1984-0.2451-0.6625-0.19720.29640.0428-0.20230.19020.65720.19870.1582-0.01040.01060.31580.05330.255943.5628-20.114829.9224
136.21512.25522.78243.1778-0.87218.0778-0.12790.65610.402-0.453-0.00840.5499-0.2003-1.23630.12980.37040.0464-0.05060.661-0.00820.29190.2542-34.199719.1088
144.28180.5050.19232.72250.27213.14320.01960.1027-0.2802-0.2396-0.0759-0.35640.04240.16430.03940.0958-0.03660.03110.15020.01910.25715.6936-38.928336.1195
155.6016-2.94474.5312.65810.0759.11490.2108-0.8051-0.11650.6896-0.2307-0.84570.30421.19420.06450.9896-0.3313-0.27581.3250.2510.62521.359-37.879766.9169
163.04920.44012.31122.84711.61992.72590.0352-0.6435-0.0580.9727-0.0042-0.42930.0165-0.0587-0.03250.9636-0.567-0.2111.71150.17780.393112.7796-35.713771.4135
174.33-0.36253.18363.83820.94073.9602-0.2595-1.02080.25411.0425-0.3038-0.7569-0.79680.38790.44550.6021-0.1983-0.10960.949-0.25950.41496.2873-24.484857.4039
180.92850.33041.32460.11840.47791.85890.1801-1.19610.43690.3401-0.390.3234-0.1517-0.52720.32820.4355-0.2577-0.02381.0973-0.38790.39630.2243-31.255458.3875
192.3380.74870.26790.3627-0.24910.94980.3995-0.761.03970.2242-0.32840.8552-0.0711-0.33660.03420.3311-0.0742-0.04140.6281-0.46490.9768-9.4472-24.984550.2435
206.4781-2.3873.40143.85151.33926.4780.2995-0.59640.28370.3544-0.39640.72380.1591-0.66640.10830.2196-0.11120.00780.4432-0.17120.2875-1.6486-33.134547.3989
215.0092-0.4559-0.09214.15590.71013.10650.369-0.9004-0.85840.7817-0.31610.80510.7346-0.7498-0.07930.5641-0.26760.07170.47950.02390.4415-0.6633-44.606548.5522
228.26822.1368-2.2941.82941.11752.98230.1563-0.24010.5752-0.41240.0275-0.0014-0.61550.2732-0.19270.4067-0.1923-0.00480.459-0.06750.269913.762-27.358848.8787
231.01780.5164-0.38324.678-6.29048.5568-0.24050.0673-0.3146-0.29730.43070.39010.6431-0.3564-0.19161.7730.00020.48011.83320.14290.87260.8971-28.026477.6897
242.5623-0.4529-1.76451.07031.23455.3989-0.24370.4165-0.66190.2288-0.18890.2971.16380.09840.44941.8401-0.06560.74661.4546-0.25410.802257.9455-26.390968.5778
252.6036-1.3655-1.83743.61780.8584.2865-0.57370.435-1.22010.5162-0.35790.54891.6948-0.09730.87912.2052-0.64150.86181.7604-0.85151.591242.388-30.691880.8729
260.6483-0.2258-0.43020.10750.36392.01470.0330.2765-0.3484-0.092-0.38280.42560.4058-0.72740.37341.6902-0.67930.8121.8755-0.94341.091838.8977-19.638584.7388
271.9068-1.4903-0.55032.29342.72214.8045-0.5036-0.1298-0.1061-0.2330.2876-0.1509-0.02480.2017-0.13731.3037-0.24180.55641.3491-0.60081.02546.8874-11.590390.5659
284.88380.715-3.86164.4105-0.32598.8064-0.5286-0.3353-0.52470.0579-0.16120.23671.33350.29430.62391.8098-0.5131.04761.4445-0.4381.440149.0234-23.195790.561
293.8224-0.8223-0.99678.61395.61994.493-0.4937-0.4126-0.0957-0.2785-0.09170.2310.2386-0.39130.52531.7201-0.23190.41152.2157-0.33430.872737.6101-19.0708116.4984
303.36024.95762.34317.47852.48947.28590.7206-1.30750.37591.0269-0.59510.7470.0269-0.0849-0.1231.8753-0.50380.52571.8287-0.24121.27341.2427-23.4353116.8826
316.45826.3457-1.89396.247-1.94131.05120.278-1.236-0.25521.0417-0.49140.47850.1431-0.4130.16192.07870.06390.9072.03140.17131.295544.1308-20.5725127.8925
325.4119-1.3902-0.76530.4461-0.030.6853-0.562-1.806-1.11590.66510.08980.59991.3938-0.51570.49752.1587-0.1330.92632.16970.04061.205149.1191-24.6063120.065
337.15030.4865-4.81492.7742-2.18225.32370.1381-0.895-0.25610.7908-0.77240.91790.8027-1.3110.56922.5235-0.43381.02591.3514-0.08691.604851.1423-34.8091108.4996
340.41190.1779-0.63330.9515-0.45632.1035-0.1352-0.2208-0.5307-0.1942-0.1774-0.4360.30520.1080.2862.3096-0.10011.15371.88490.27081.522157.4345-28.4056109.5227
351.6006-0.1133-1.19560.7297-1.28673.97720.0611-0.3025-0.2853-0.031-0.336-0.33370.68740.2060.27532.3651-0.03131.01391.21180.2531.314764.3819-30.726499.9826
363.28450.7724-1.90370.9668-1.82553.5174-0.03540.05020.00140.2229-0.2167-0.04230.03410.3853-0.01751.7924-0.24831.0191.25870.12421.075260.6319-18.145599.0113
373.62941.3548-2.10831.9742-0.49983.2397-0.31040.0366-0.3996-0.1433-0.07440.00280.6148-0.67280.36012.2-0.37351.14881.3378-0.30411.278350.745-24.397398.8184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 58 )A46 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 82 )A59 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 107 )A83 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 125 )A108 - 125
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 153 )A126 - 153
6X-RAY DIFFRACTION6chain 'A' and (resid 154 through 168 )A154 - 168
7X-RAY DIFFRACTION7chain 'A' and (resid 169 through 204 )A169 - 204
8X-RAY DIFFRACTION8chain 'A' and (resid 205 through 223 )A205 - 223
9X-RAY DIFFRACTION9chain 'A' and (resid 224 through 246 )A224 - 246
10X-RAY DIFFRACTION10chain 'A' and (resid 250 through 256 )A250 - 256
11X-RAY DIFFRACTION11chain 'B' and (resid 46 through 114 )B46 - 114
12X-RAY DIFFRACTION12chain 'B' and (resid 115 through 246 )B115 - 246
13X-RAY DIFFRACTION13chain 'C' and (resid 46 through 107 )C46 - 107
14X-RAY DIFFRACTION14chain 'C' and (resid 108 through 246 )C108 - 246
15X-RAY DIFFRACTION15chain 'D' and (resid 46 through 71 )D46 - 71
16X-RAY DIFFRACTION16chain 'D' and (resid 72 through 107 )D72 - 107
17X-RAY DIFFRACTION17chain 'D' and (resid 108 through 125 )D108 - 125
18X-RAY DIFFRACTION18chain 'D' and (resid 126 through 157 )D126 - 157
19X-RAY DIFFRACTION19chain 'D' and (resid 158 through 169 )D158 - 169
20X-RAY DIFFRACTION20chain 'D' and (resid 170 through 199 )D170 - 199
21X-RAY DIFFRACTION21chain 'D' and (resid 200 through 232 )D200 - 232
22X-RAY DIFFRACTION22chain 'D' and (resid 233 through 250 )D233 - 250
23X-RAY DIFFRACTION23chain 'E' and (resid 46 through 58 )E46 - 58
24X-RAY DIFFRACTION24chain 'E' and (resid 59 through 107 )E59 - 107
25X-RAY DIFFRACTION25chain 'E' and (resid 108 through 125 )E108 - 125
26X-RAY DIFFRACTION26chain 'E' and (resid 126 through 189 )E126 - 189
27X-RAY DIFFRACTION27chain 'E' and (resid 190 through 218 )E190 - 218
28X-RAY DIFFRACTION28chain 'E' and (resid 219 through 246 )E219 - 246
29X-RAY DIFFRACTION29chain 'F' and (resid 46 through 69 )F46 - 69
30X-RAY DIFFRACTION30chain 'F' and (resid 70 through 83 )F70 - 83
31X-RAY DIFFRACTION31chain 'F' and (resid 84 through 95 )F84 - 95
32X-RAY DIFFRACTION32chain 'F' and (resid 96 through 107 )F96 - 107
33X-RAY DIFFRACTION33chain 'F' and (resid 108 through 125 )F108 - 125
34X-RAY DIFFRACTION34chain 'F' and (resid 126 through 156 )F126 - 156
35X-RAY DIFFRACTION35chain 'F' and (resid 157 through 188 )F157 - 188
36X-RAY DIFFRACTION36chain 'F' and (resid 189 through 218 )F189 - 218
37X-RAY DIFFRACTION37chain 'F' and (resid 219 through 246 )F219 - 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