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- PDB-6xk2: Crystal structure of Ribokinase from Cryptococcus neoformans var.... -

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Basic information

Entry
Database: PDB / ID: 6xk2
TitleCrystal structure of Ribokinase from Cryptococcus neoformans var. grubii serotype A in complex with ADP
ComponentsRibokinase
KeywordsTRANSFERASE / SSGCID / Cryptococcus neoformans / Ribokinase / phosphorylation / ATP / ADP / D-ribose / D-ribose 5-phosphate / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Ribokinase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Ribokinase from Cryptococcus neoformans var. grubii serotype A in complex with ADP
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Ribokinase
B: Ribokinase
C: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,31114
Polymers140,3474
Non-polymers1,96410
Water3,009167
1
A: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1367
Polymers70,1732
Non-polymers9625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-41 kcal/mol
Surface area24920 Å2
MethodPISA
2
B: Ribokinase
C: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1757
Polymers70,1732
Non-polymers1,0025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-27 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.170, 84.570, 98.270
Angle α, β, γ (deg.)90.000, 95.270, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 5 or (resid 6...
21(chain B and (resid 4 through 5 or (resid 6...
31(chain C and (resid 4 through 5 or (resid 6...
41(chain D and (resid 4 through 88 or (resid 89...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 5 or (resid 6...A4 - 5
121(chain A and (resid 4 through 5 or (resid 6...A6
131(chain A and (resid 4 through 5 or (resid 6...A2 - 323
141(chain A and (resid 4 through 5 or (resid 6...A2 - 323
151(chain A and (resid 4 through 5 or (resid 6...A2 - 323
161(chain A and (resid 4 through 5 or (resid 6...A2 - 323
211(chain B and (resid 4 through 5 or (resid 6...B4 - 5
221(chain B and (resid 4 through 5 or (resid 6...B6
231(chain B and (resid 4 through 5 or (resid 6...B4 - 323
241(chain B and (resid 4 through 5 or (resid 6...B4 - 323
251(chain B and (resid 4 through 5 or (resid 6...B4 - 323
261(chain B and (resid 4 through 5 or (resid 6...B4 - 323
311(chain C and (resid 4 through 5 or (resid 6...C4 - 5
321(chain C and (resid 4 through 5 or (resid 6...C6
331(chain C and (resid 4 through 5 or (resid 6...C4 - 401
341(chain C and (resid 4 through 5 or (resid 6...C4 - 401
351(chain C and (resid 4 through 5 or (resid 6...C4 - 401
411(chain D and (resid 4 through 88 or (resid 89...D4 - 88
421(chain D and (resid 4 through 88 or (resid 89...D89 - 90
431(chain D and (resid 4 through 88 or (resid 89...D4 - 400
441(chain D and (resid 4 through 88 or (resid 89...D4 - 400
451(chain D and (resid 4 through 88 or (resid 89...D4 - 400
461(chain D and (resid 4 through 88 or (resid 89...D4 - 400

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Components

#1: Protein
Ribokinase / / RK


Mass: 35086.723 Da / Num. of mol.: 4 / Fragment: CrneC.01141.a.B12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02296 / Plasmid: CrneC.01141.a.B12
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: J9VQ51, ribokinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: 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

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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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic MCSG-1 screen D12: 20% (w/V) PDG 3350, 200mM ammonium chloride; CrneC.01141.a.B12.PW38396 at 19.46mg/ml + 2.5mM ADP + 2.5mM MgCl2; tray 299998 D12; cryo: 20% EG + 2.5mM ADP/MgCl2; puck pjn0-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 12, 2018 / Details: C(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→37.05 Å / Num. obs: 43388 / % possible obs: 99.1 % / Redundancy: 3.413 % / Biso Wilson estimate: 58.322 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.055 / Χ2: 1.029 / Net I/σ(I): 17.97 / Num. measured all: 148087 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.563.4270.5752.0911007321532120.80.68299.9
2.56-2.643.4270.4262.7910658311931100.8730.50699.7
2.64-2.713.4170.3363.4710491307330700.9090.39999.9
2.71-2.83.4230.2494.5110035293929320.9630.29699.8
2.8-2.893.4280.1796.159917290028930.9780.21399.8
2.89-2.993.4030.1368.19430277227710.9870.162100
2.99-3.13.4310.1099.969196269226800.9920.12999.6
3.1-3.233.4180.08512.718767257425650.9940.10199.7
3.23-3.373.4210.06716.598480250024790.9960.07999.2
3.37-3.543.4060.05220.648007236523510.9970.06299.4
3.54-3.733.4110.04225.567626225822360.9980.04999
3.73-3.953.4150.03629.227274214921300.9990.04299.1
3.95-4.233.4170.03232.616741200219730.9980.03898.6
4.23-4.563.3920.02836.826279188018510.9990.03398.5
4.56-53.40.02539.315800173517060.9990.0398.3
5-5.593.4190.02638.15238156115320.9990.03198.1
5.59-6.463.4030.02737.544648139913660.9990.03297.6
6.46-7.913.4010.02145.53891117211440.9990.02497.6
7.91-11.183.3780.01650.87304492790110.01997.2
11.18-37.053.2060.01650.8815585314860.9990.0291.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure, 6cw5
Resolution: 2.5→37.05 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 1941 4.48 %0
Rwork0.1811 41396 --
obs0.1833 43337 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.25 Å2 / Biso mean: 65.7744 Å2 / Biso min: 34.2 Å2
Refinement stepCycle: final / Resolution: 2.5→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9027 0 123 167 9317
Biso mean--62.28 54.46 -
Num. residues----1266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069333
X-RAY DIFFRACTIONf_angle_d0.82712762
X-RAY DIFFRACTIONf_dihedral_angle_d14.9913241
X-RAY DIFFRACTIONf_chiral_restr0.0481510
X-RAY DIFFRACTIONf_plane_restr0.0061705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5225X-RAY DIFFRACTION6.196TORSIONAL
12B5225X-RAY DIFFRACTION6.196TORSIONAL
13C5225X-RAY DIFFRACTION6.196TORSIONAL
14D5225X-RAY DIFFRACTION6.196TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.560.321500.27729333083100
2.56-2.630.32141480.261729303078100
2.63-2.710.30361320.25429883120100
2.71-2.80.32451390.240729403079100
2.8-2.90.29041500.234229563106100
2.9-3.010.27511430.214829683111100
3.01-3.150.25861210.21962966308799
3.15-3.320.29061330.210329723105100
3.32-3.520.25751320.18962979311199
3.52-3.790.19521290.17762936306599
3.79-4.180.22351430.16562955309899
4.18-4.780.17961300.14082967309799
4.78-6.020.221360.15842953308998
6.02-37.050.18471550.14932953310897
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)
14.84030.3021-3.21461.9878-0.62214.17370.0056-0.0846-0.0611-0.1234-0.1374-0.13460.00460.48510.10430.3441-0.0028-0.02960.3344-0.01260.3212-5.1721-27.4283-25.3242
24.298-0.2437-1.38992.69090.47644.31050.12860.67560.3409-0.4692-0.03220.4939-0.542-0.3542-0.17970.4240.0328-0.04960.45210.1160.4487-22.056-19.4523-27.1262
32.6373-0.28270.12831.44120.43113.98590.29250.40550.957-0.23180.09820.3998-0.8278-0.222-0.25680.75230.0460.1380.35010.07820.901-21.4727-6.0682-18.8371
44.40610.69470.81823.3423-0.66313.74690.1185-0.34870.47320.1641-0.0225-0.0899-0.03130.2431-0.11590.4461-0.02450.05160.3857-0.10370.3463-10.9859-18.3083-8.5934
55.40070.11681.39540.45210.42462.87040.0083-0.1105-0.60290.03910.19170.03040.20930.3779-0.21860.36750.071-0.03030.3465-0.11990.5361-39.449-15.87235.1649
67.5396-0.14580.17351.05791.19252.36980.06260.6997-0.1562-0.13450.0020.1756-0.04570.6761-0.00010.3791-0.00970.00930.4257-0.05060.5013-43.525-9.6387-3.1921
73.8628-1.01352.33751.34850.54993.5853-0.09130.33410.8752-0.1749-0.11-0.1251-0.41180.51560.08980.4586-0.03110.03940.36550.03990.602-47.213-0.6847-1.8837
83.2377-0.77991.72271.77240.79953.3991-0.09440.1005-0.01920.13410.1307-0.30870.14640.1671-0.11460.33260.0343-0.01550.3425-0.05350.4845-43.8636-8.8586.997
91.9586-0.26720.911.23220.94451.50910.1904-0.3401-0.21610.1525-0.0050.4281-0.3172-0.61790.37320.50420.08590.03040.477-0.010.6577-62.8875-1.06495.8737
103.8893-0.18630.72983.30081.17034.06770.1984-0.2574-0.94060.1694-0.16320.54590.3976-0.3059-0.04390.3792-0.03310.04030.38850.02750.7675-60.924-17.42514.5411
112.8414-1.3898-0.91010.98410.97421.34090.1150.2878-1.53830.0767-0.18130.82390.2738-0.19980.12930.6466-0.1144-0.06850.5523-0.10241.4423-60.2857-32.94651.2973
122.86320.61980.03163.39870.30822.02220.1180.9121-1.1261-0.2729-0.14880.13270.147-0.01080.0310.4450.0597-0.06970.5523-0.27170.7679-51.9782-21.7356-11.8586
137.2588-2.565-1.45096.69920.92091.14070.76231.0540.1296-0.5277-0.3614-1.14360.1068-0.0203-0.43880.47920.1010.05070.68070.0130.734-43.8232-12.3823-15.4409
149.39950.84952.89542.2808-0.06751.94790.151-0.6535-0.91890.1031-0.01290.15650.0977-0.1338-0.12150.45110.08270.01130.49440.060.4927-30.1027-15.922318.7432
156.60721.46631.17413.48060.26231.72150.1142-0.36260.44110.2773-0.1653-0.0672-0.2374-0.07190.01660.43230.06660.03930.5391-0.02110.3544-20.1222-5.968723.5164
168.70851.82883.30153.05940.81692.03870.28420.16-0.1927-0.1669-0.13340.0914-0.00590.1626-0.12410.48780.11840.01520.53230.03110.3147-23.5874-11.78115.6547
172.9731-0.61021.74784.3353-0.05834.27460.27670.2327-0.1442-0.4054-0.4432-0.73010.0380.7213-0.02760.37650.0633-0.0020.7103-0.01630.6446-6.6252-15.201617.7229
181.90860.6542-0.11163.1022-0.67554.27240.5207-0.3222-2.6407-0.0821-0.3099-0.57540.99050.37570.07750.70360.1444-0.2480.57730.14311.4969-13.4408-30.448724.0392
197.5422-2.1001-0.97621.57630.11444.15950.5477-0.1963-1.93350.3459-0.1068-0.11460.80930.1868-0.27870.82740.0702-0.21320.83780.32771.4234-14.3422-32.428830.1118
200.52980.53940.24251.5691-0.23132.2029-0.6614-1.5614-1.22980.84030.5959-0.00940.4444-0.1021-0.17230.7061-0.04920.0281.14880.50760.8212-25.3211-23.724337.1428
210.56910.07911.50652.14490.46873.97570.7712-1.8039-1.63370.3822-0.1505-0.18220.03410.30880.00930.6549-0.067-0.11520.99470.2160.4416-14.4698-16.885235.325
220.6449-0.15670.92970.97580.72012.89040.0284-0.8112-0.54780.9775-0.18940.28360.39320.1638-0.48320.810.0208-0.04261.35330.54730.5292-21.8577-18.739.153
234.64341.81820.58772.8104-1.8394.10650.3129-1.08270.2390.4695-0.20930.179-0.9091-0.1841-0.12310.7788-0.09880.09821.07530.12060.4852-25.1096-9.687437.7028
247.683-0.5287-3.37510.34020.05343.2440.35220.73450.13520.0049-0.3752-0.1292-0.1809-0.2131-0.04390.4353-0.0128-0.00420.47950.1230.477810.765-25.7652-42.4386
257.9655-3.6517-3.28642.34171.80252.1215-0.3796-0.1721-1.14530.1345-0.49130.64240.51470.11020.62240.5623-0.01180.00930.60740.14430.871417.7085-38.0727-41.8554
264.3096-0.9163-1.16033.06630.18092.03140.26390.82610.6859-0.4388-0.3578-0.4475-0.08760.24720.14960.54140.03710.13380.63410.25170.552211.3121-25.9978-37.5969
272.38210.6692-0.45713.35040.05034.46760.3386-1.2128-0.83540.233-0.1162-0.25280.4460.7165-0.10970.49520.0161-0.0941.02310.27280.632330.2344-29.7883-36.5068
284.94791.3343-0.7294.4255-0.23924.73540.1212-0.44930.4692-0.0765-0.3241-0.5374-0.64230.72980.1380.4252-0.09750.00990.66850.1120.525133.7136-15.0615-47.0848
296.04880.550.91312.44130.22552.76910.12050.51430.2527-0.0898-0.2199-0.1687-0.08450.80120.1690.44280.07480.07320.77560.15230.425329.1086-22.9875-57.4355
303.4195-1.21780.64795.2710.6710.27710.5750.1174-0.4177-0.7418-0.27430.90050.865-0.657-0.25960.82180.1115-0.09610.6181-0.00550.744217.5808-32.9127-60.3732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 116 )A2 - 116
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 208 )A117 - 208
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 247 )A209 - 247
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 323 )A248 - 323
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 34 )B4 - 34
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 53 )B35 - 53
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 78 )B54 - 78
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 116 )B79 - 116
9X-RAY DIFFRACTION9chain 'B' and (resid 117 through 131 )B117 - 131
10X-RAY DIFFRACTION10chain 'B' and (resid 132 through 197 )B132 - 197
11X-RAY DIFFRACTION11chain 'B' and (resid 198 through 233 )B198 - 233
12X-RAY DIFFRACTION12chain 'B' and (resid 234 through 305 )B234 - 305
13X-RAY DIFFRACTION13chain 'B' and (resid 306 through 323 )B306 - 323
14X-RAY DIFFRACTION14chain 'C' and (resid 4 through 34 )C4 - 34
15X-RAY DIFFRACTION15chain 'C' and (resid 35 through 78 )C35 - 78
16X-RAY DIFFRACTION16chain 'C' and (resid 79 through 116 )C79 - 116
17X-RAY DIFFRACTION17chain 'C' and (resid 117 through 152 )C117 - 152
18X-RAY DIFFRACTION18chain 'C' and (resid 153 through 224 )C153 - 224
19X-RAY DIFFRACTION19chain 'C' and (resid 225 through 247 )C225 - 247
20X-RAY DIFFRACTION20chain 'C' and (resid 248 through 270 )C248 - 270
21X-RAY DIFFRACTION21chain 'C' and (resid 271 through 288 )C271 - 288
22X-RAY DIFFRACTION22chain 'C' and (resid 289 through 305 )C289 - 305
23X-RAY DIFFRACTION23chain 'C' and (resid 306 through 323 )C306 - 323
24X-RAY DIFFRACTION24chain 'D' and (resid 4 through 53 )D4 - 53
25X-RAY DIFFRACTION25chain 'D' and (resid 54 through 78 )D54 - 78
26X-RAY DIFFRACTION26chain 'D' and (resid 79 through 111 )D79 - 111
27X-RAY DIFFRACTION27chain 'D' and (resid 112 through 152 )D112 - 152
28X-RAY DIFFRACTION28chain 'D' and (resid 153 through 224 )D153 - 224
29X-RAY DIFFRACTION29chain 'D' and (resid 225 through 304 )D225 - 304
30X-RAY DIFFRACTION30chain 'D' and (resid 305 through 323 )D305 - 323

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