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- PDB-6c8q: Crystal structure of NAD synthetase (NadE) from Enterococcus faec... -

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Basic information

Entry
Database: PDB / ID: 6c8q
TitleCrystal structure of NAD synthetase (NadE) from Enterococcus faecalis in complex with NAD+
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsTRANSFERASE / NAD / NadE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP PYROPHOSPHATASE / LIGASE / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
NH(3)-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesEnterococcus faecalis V583 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.583 Å
AuthorsStogios, P.J. / Skarina, T. / McChesney, C. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: To be published
Authors: Stogios, P.J.
History
DepositionJan 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NH(3)-dependent NAD(+) synthetase
B: NH(3)-dependent NAD(+) synthetase
C: NH(3)-dependent NAD(+) synthetase
D: NH(3)-dependent NAD(+) synthetase
E: NH(3)-dependent NAD(+) synthetase
F: NH(3)-dependent NAD(+) synthetase
G: NH(3)-dependent NAD(+) synthetase
H: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,88816
Polymers243,5818
Non-polymers5,3078
Water16,700927
1
A: NH(3)-dependent NAD(+) synthetase
B: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2224
Polymers60,8952
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-60 kcal/mol
Surface area23040 Å2
MethodPISA
2
C: NH(3)-dependent NAD(+) synthetase
G: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2224
Polymers60,8952
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-58 kcal/mol
Surface area22500 Å2
MethodPISA
3
D: NH(3)-dependent NAD(+) synthetase
F: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2224
Polymers60,8952
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-60 kcal/mol
Surface area22420 Å2
MethodPISA
4
E: NH(3)-dependent NAD(+) synthetase
H: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2224
Polymers60,8952
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-59 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.445, 85.165, 175.811
Angle α, β, γ (deg.)90.00, 94.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NH(3)-dependent NAD(+) synthetase


Mass: 30447.574 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis V583 (bacteria) / Strain: ATCC 700802 / V583 / Gene: nadE, EF_2625 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q830Y9, NAD+ synthase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 927 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-tris pH 5.5, 0.2 M magnesium chloride, 25% (w/v) PEG3350, 10 mM NAD+

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 77971 / % possible obs: 99.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.076 / Net I/σ(I): 7.8
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 3667 / CC1/2: 0.651 / Rpim(I) all: 0.495 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5huj
Resolution: 2.583→24.776 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2018 2.59 %RANDOM
Rwork0.1875 ---
obs0.1888 77904 98.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.583→24.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16539 0 335 927 17801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217283
X-RAY DIFFRACTIONf_angle_d0.5423426
X-RAY DIFFRACTIONf_dihedral_angle_d21.2366464
X-RAY DIFFRACTIONf_chiral_restr0.0392622
X-RAY DIFFRACTIONf_plane_restr0.0033005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5828-2.64730.31961250.29794639X-RAY DIFFRACTION85
2.6473-2.71880.32791410.2685373X-RAY DIFFRACTION98
2.7188-2.79870.29451340.25485438X-RAY DIFFRACTION99
2.7987-2.88890.30671540.25785408X-RAY DIFFRACTION99
2.8889-2.9920.34681390.23915424X-RAY DIFFRACTION99
2.992-3.11160.29131490.23525451X-RAY DIFFRACTION99
3.1116-3.25290.3291440.23915473X-RAY DIFFRACTION99
3.2529-3.4240.28931440.21935477X-RAY DIFFRACTION100
3.424-3.63790.25081470.18765446X-RAY DIFFRACTION100
3.6379-3.91780.23751520.17395516X-RAY DIFFRACTION100
3.9178-4.31020.18841460.14815530X-RAY DIFFRACTION100
4.3102-4.92960.16211500.13075489X-RAY DIFFRACTION100
4.9296-6.19470.20521420.16515574X-RAY DIFFRACTION100
6.1947-24.77750.20161510.15925648X-RAY DIFFRACTION100
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)
10.8998-0.66970.32560.7903-0.03931.37440.0140.09610.1043-0.0649-0.0004-0.1565-0.23380.0251-0.01050.3933-0.04380.00010.28630.03150.495519.94681.29923.0909
20.8403-0.16220.7982.01540.79771.22060.0285-0.01560.22540.0282-0.05840.1049-0.0429-0.0890.02210.2619-0.00140.03970.26090.02320.356811.7273-9.92784.199
32.49063.6204-0.29838.2701-1.31240.2980.2391-0.09110.50342.02580.43671.1109-0.6895-0.908-0.75540.6750.17250.16830.56570.07340.7066.50866.552418.777
43.1455-3.5111-1.84365.80242.71632.86440.0477-0.1858-0.06920.29580.0125-0.1708-0.0508-0.0633-0.04810.336-0.05-0.00130.26370.03420.363519.7175-13.752821.9107
57.30725.5717-4.95845.2326-4.97374.72780.7989-0.19350.05540.2316-1.2538-1.8944-0.35650.61440.47630.45840.0518-0.01590.55840.12850.655642.8628-27.39491.0981
62.0066-0.712-0.30042.0948-0.71072.3569-0.067-0.0661-0.2504-0.13250.0474-0.19210.210.02790.02920.35550.04310.01950.24870.02950.468421.4369-38.14539.6148
74.2195-0.8438-0.58217.22830.0530.6591-0.01530.3468-0.5433-0.9139-0.09320.11920.4417-0.18810.0860.3655-0.04110.04670.2889-0.10520.42411.2972-38.1106-2.4478
81.4553-0.17010.91560.6321-0.14571.0452-0.09610.1635-0.0019-0.19420.0441-0.08790.07630.10120.06070.3578-0.01020.06240.2387-0.00970.382317.4019-26.136-3.6527
97.29267.2701-7.21279.2499-7.97257.4165-1.19350.4533-0.5466-2.07630.7916-1.60581.83710.57890.48610.9037-0.06340.16420.6748-0.15380.630227.039-42.4369-12.7906
101.4479-0.6994-1.81252.72211.81043.2532-0.32150.0676-0.1303-0.18020.1687-0.2260.24380.22860.12880.3743-0.00950.11370.36610.05720.554536.1179-20.3355-6.5176
118.0853-1.1585-6.01562.92762.74877.5534-0.6346-0.0257-0.7427-0.0892-0.00050.54480.5267-0.25980.65050.435-0.05290.05660.31190.0120.4133-16.3056-30.220232.4579
124.49820.8262-3.34044.0625-1.56086.99840.02180.04120.15190.15790.0930.33250.1645-0.3212-0.07730.39250.12790.04040.472-0.01920.4132-23.8084-15.537339.5505
138.2817-0.73213.16254.1873.07274.447-0.21360.69570.4914-0.45050.07050.2076-0.2592-0.21390.12470.43650.19430.030.39860.0390.3003-19.5899-4.572935.4536
140.964-0.26490.26650.98681.07111.6617-0.110.02040.0474-0.0640.0350.0396-0.1343-0.13880.06810.43670.04910.06390.37740.08460.346-7.6346-10.98837.1843
157.5281.569-5.43310.3718-1.15244.10090.51421.21050.62860.1078-0.00640.1694-0.6619-0.6907-0.49330.5650.0788-0.01780.4894-0.03060.5525-10.1766-14.151819.2175
160.6267-0.27581.7630.1517-0.59475.9507-0.0362-0.0245-0.07650.01420.00420.01460.2492-0.28560.01460.45480.03280.04870.3478-0.02190.50091.324-28.253729.9714
172.5616-1.011-1.80452.5061.31787.22520.0838-0.43430.45610.1938-0.22440.1857-0.6471-0.22040.1750.52780.08580.02420.7101-0.2240.5903-32.26911.417285.1933
180.17921.21-0.06218.49421.28615.4901-0.6587-1.26530.55480.61630.5876-1.3318-0.76920.5064-0.0720.76490.0679-0.17651.0403-0.22880.6652-16.1583-0.299293.5035
193.0994-1.4945-0.58863.48970.01551.5839-0.1461-0.87320.25360.30960.0854-0.23580.05060.05120.04950.4751-0.01190.00660.7522-0.07910.4034-19.8603-10.756486.0381
204.6978-5.6012-5.40796.69346.6588.00580.3446-0.15060.8431-0.39360.15-0.5659-1.31540.9884-0.47590.8704-0.12170.08130.6178-0.00860.5637-19.28970.169169.0248
211.07191.9288-1.84525.5911-3.29474.1464-0.08320.422-0.0163-0.33910.11560.3679-0.0018-0.6517-0.07790.54430.0663-0.00380.6736-0.06880.5973-30.4189-18.401569.3577
221.89510.1036-0.18171.50440.3925.74710.014-0.08380.0521-0.02160.19350.2817-0.6097-0.2239-0.15360.42980.07350.00350.27370.06550.459628.4632-48.831930.8112
237.5257-3.53591.15494.00060.06891.41970.1209-0.5192-0.80670.01270.39140.90060.2064-0.4743-0.52560.4811-0.0409-0.02560.28290.00090.536623.455-66.781729.7104
241.4084-0.7435-0.43592.423-0.331.5172-0.0615-0.2796-0.24860.16180.23090.34340.0327-0.1216-0.16460.48780.04890.0430.34490.04610.508532.3845-63.394638.9567
258.91910.44266.85030.0550.4255.37180.0504-1.354-0.34560.24080.36860.5790.0547-1.5353-0.73950.65740.00860.12760.54630.1860.815717.6956-56.700645.9452
268.8104-2.2464-0.72131.2154-0.98281.6329-0.2622-0.61620.34420.54160.3705-0.0727-0.4019-0.3243-0.14370.68290.17280.0020.5195-0.07370.46735.548-47.883552.1662
277.7894-4.558-4.00354.31943.86643.806-0.01320.6025-1.1335-0.0514-0.21351.3490.1201-0.64050.40510.6637-0.15860.20120.7776-0.06270.9812-43.7923-32.565880.4741
283.24430.03191.96436.694-1.18791.3428-0.07370.0852-1.06070.03910.06220.21940.60260.22550.22250.75360.03680.27830.61710.05340.7436-24.9229-38.396879.3263
292.00121.9605-0.38478.20081.41880.7737-0.4256-1.0425-0.64061.5912-0.052-0.50261.4252-0.50540.79961.35140.30040.16951.24240.34351.1126-21.4415-39.811297.7339
303.97720.336-0.6113.3614-0.49720.9182-0.3203-0.8481-0.42850.80450.03430.26770.5444-0.01720.31590.7580.01550.16160.84140.14820.5274-26.4263-27.382992.1347
313.36972.15-2.14812.3203-1.46842.3765-0.0527-0.8925-0.35260.4175-0.09910.68490.496-0.1033-0.15350.7958-0.04990.27741.0302-0.01510.9255-43.4692-24.995295.1776
323.1163-0.2361-1.63720.38260.36633.1194-0.1409-0.2764-0.32390.10080.0167-0.13110.20640.1650.15340.48590.12650.02080.33330.02560.39259.8696-28.173253.4125
335.645-0.23240.65093.2439-1.71634.4052-0.0198-0.80480.1470.4710.0183-0.3703-0.01520.2907-0.0150.3474-0.0305-0.02850.37890.02250.31916.1099-11.524554.1613
341.68-1.7960.86263.0176-1.20980.5881-0.1235-0.28540.0640.2650.13960.1139-0.2629-0.2025-0.010.46680.06140.03020.3713-0.0140.32770.3542-13.232653.4955
354.57160.9441-0.05972.2223-0.97640.47060.4726-1.2562-0.08451.3693-0.37310.72380.3880.2982-0.10951.1493-0.02980.18310.6946-0.10890.722110.1459-16.233272.0947
360.5907-0.20661.21230.2292-1.49115.8475-0.0294-0.2816-0.22230.25460.00870.21090.5521-0.0998-0.0220.56980.01760.09080.5310.08940.5038-8.8275-27.32760.6559
372.81261.245-2.17592.5925-2.73153.15940.1384-0.45150.29140.57020.1051-0.4933-0.64190.069-0.190.49730.008-0.10580.4539-0.13820.530361.6465-49.68644.3514
386.1778-4.2885-3.73066.721.19116.9314-0.1862-0.2478-0.07560.46330.15610.2397-0.7038-0.01250.02610.56360.1322-0.11270.4812-0.06030.413151.7064-64.240552.7937
392.6794-0.2860.2561.8069-0.41071.30010.0008-0.2115-0.10940.30470.0715-0.11870.19730.3823-0.07910.44750.1261-0.00710.4078-0.0260.367254.0858-68.129442.4417
400.575-1.97722.37076.8204-8.00979.8981-0.41820.66170.6511-1.2626-0.1707-0.18280.74982.28270.48360.80010.1672-0.06551.06790.01750.707172.0153-67.651335.1435
414.74010.42890.0047.53053.10072.4862-0.2101-0.1763-0.3016-0.09440.1085-0.3934-0.08860.54970.14490.39570.04020.07890.49980.07440.445962.2385-53.163524.5635
428.5646-1.6867-3.23351.01442.55276.5040.274-0.19710.2437-0.17120.158-0.3165-0.82020.3941-0.46560.43240.0127-0.03510.2796-0.03540.407741.8964-47.609531.4439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 199 )
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 222 )
4X-RAY DIFFRACTION4chain 'A' and (resid 223 through 275 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 19 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 72 )
7X-RAY DIFFRACTION7chain 'B' and (resid 73 through 102 )
8X-RAY DIFFRACTION8chain 'B' and (resid 103 through 199 )
9X-RAY DIFFRACTION9chain 'B' and (resid 200 through 222 )
10X-RAY DIFFRACTION10chain 'B' and (resid 223 through 275 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 37 )
12X-RAY DIFFRACTION12chain 'C' and (resid 38 through 72 )
13X-RAY DIFFRACTION13chain 'C' and (resid 73 through 102 )
14X-RAY DIFFRACTION14chain 'C' and (resid 103 through 199 )
15X-RAY DIFFRACTION15chain 'C' and (resid 200 through 231 )
16X-RAY DIFFRACTION16chain 'C' and (resid 232 through 275 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 72 )
18X-RAY DIFFRACTION18chain 'D' and (resid 73 through 102 )
19X-RAY DIFFRACTION19chain 'D' and (resid 103 through 199 )
20X-RAY DIFFRACTION20chain 'D' and (resid 200 through 245 )
21X-RAY DIFFRACTION21chain 'D' and (resid 246 through 275 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 72 )
23X-RAY DIFFRACTION23chain 'E' and (resid 73 through 102 )
24X-RAY DIFFRACTION24chain 'E' and (resid 103 through 199 )
25X-RAY DIFFRACTION25chain 'E' and (resid 200 through 231 )
26X-RAY DIFFRACTION26chain 'E' and (resid 232 through 275 )
27X-RAY DIFFRACTION27chain 'F' and (resid 1 through 37 )
28X-RAY DIFFRACTION28chain 'F' and (resid 38 through 83 )
29X-RAY DIFFRACTION29chain 'F' and (resid 84 through 102 )
30X-RAY DIFFRACTION30chain 'F' and (resid 103 through 199 )
31X-RAY DIFFRACTION31chain 'F' and (resid 200 through 275 )
32X-RAY DIFFRACTION32chain 'G' and (resid 2 through 51 )
33X-RAY DIFFRACTION33chain 'G' and (resid 52 through 112 )
34X-RAY DIFFRACTION34chain 'G' and (resid 113 through 199 )
35X-RAY DIFFRACTION35chain 'G' and (resid 200 through 222 )
36X-RAY DIFFRACTION36chain 'G' and (resid 223 through 275 )
37X-RAY DIFFRACTION37chain 'H' and (resid 2 through 37 )
38X-RAY DIFFRACTION38chain 'H' and (resid 38 through 51 )
39X-RAY DIFFRACTION39chain 'H' and (resid 52 through 199 )
40X-RAY DIFFRACTION40chain 'H' and (resid 200 through 222 )
41X-RAY DIFFRACTION41chain 'H' and (resid 223 through 258 )
42X-RAY DIFFRACTION42chain 'H' and (resid 259 through 275 )

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