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- PDB-5zdc: Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from ... -

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Basic information

Entry
Database: PDB / ID: 5zdc
TitleCrystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P32)
Componentspoly ADP-ribose glycohydrolase
KeywordsHYDROLASE / ADP-ribose / poly(ADP-ribose) glycohydrolase
Function / homology
Function and homology information


Conserved hypothetical protein CHP02452 / Microbial-type PARG, catalytic domain / Microbial-type PARG, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / PHOSPHATE ION / Microbial-type PARG catalytic domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å
AuthorsCho, C.C. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (Taiwan)105-2113-M-002-009 Taiwan
CitationJournal: Nat Commun / Year: 2019
Title: Structural and biochemical evidence supporting poly ADP-ribosylation in the bacterium Deinococcus radiodurans.
Authors: Cho, C.C. / Chien, C.Y. / Chiu, Y.C. / Lin, M.H. / Hsu, C.H.
History
DepositionFeb 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: poly ADP-ribose glycohydrolase
F: poly ADP-ribose glycohydrolase
H: poly ADP-ribose glycohydrolase
J: poly ADP-ribose glycohydrolase
L: poly ADP-ribose glycohydrolase
D: poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,24215
Polymers165,6016
Non-polymers3,6419
Water17,889993
1
C: poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2543
Polymers27,6001
Non-polymers6542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2543
Polymers27,6001
Non-polymers6542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1592
Polymers27,6001
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1592
Polymers27,6001
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
L: poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1592
Polymers27,6001
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2543
Polymers27,6001
Non-polymers6542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.498, 108.498, 130.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
poly ADP-ribose glycohydrolase


Mass: 27600.174 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_B0099 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RZM4
#2: Chemical
ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 993 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20 % 2-Propanol, 20% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.979→28.029 Å / Num. obs: 119193 / % possible obs: 99.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.112
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.408 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.979→28.029 Å / Cross valid method: THROUGHOUT / σ(F): 25.16 / Phase error: 19.67 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1905 2045 1.82 %
Rwork0.1445 --
obs0.147 112222 93.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.979→28.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11576 0 231 993 12800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812086
X-RAY DIFFRACTIONf_angle_d1.03916474
X-RAY DIFFRACTIONf_dihedral_angle_d7.8387180
X-RAY DIFFRACTIONf_chiral_restr0.0551806
X-RAY DIFFRACTIONf_plane_restr0.0062186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9808-2.02690.2682770.20884359X-RAY DIFFRACTION55
2.0269-2.07760.24651020.19915361X-RAY DIFFRACTION67
2.0776-2.13370.19361400.18747124X-RAY DIFFRACTION89
2.1337-2.19650.2461380.17637790X-RAY DIFFRACTION98
2.1965-2.26730.25291460.1717912X-RAY DIFFRACTION98
2.2673-2.34830.22621400.16027759X-RAY DIFFRACTION98
2.3483-2.44230.22081440.16267870X-RAY DIFFRACTION98
2.4423-2.55340.21411480.15487805X-RAY DIFFRACTION98
2.5534-2.68790.18311500.15447851X-RAY DIFFRACTION98
2.6879-2.85610.23061360.14767834X-RAY DIFFRACTION98
2.8561-3.07630.18751460.14277754X-RAY DIFFRACTION97
3.0763-3.38540.18411430.13157786X-RAY DIFFRACTION97
3.3854-3.8740.1641450.12297754X-RAY DIFFRACTION97
3.874-4.87610.15441440.11247664X-RAY DIFFRACTION96
4.8761-26.86220.18271310.16467387X-RAY DIFFRACTION93
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)
12.03341.1822-0.35925.16480.9572.8918-0.0852-0.0953-0.0339-0.0562-0.08710.18310.2198-0.24540.13030.15970.0261-0.00180.20040.02070.17-23.164270.3328-24.6517
28.6545-5.77191.96658.2444-0.9364.1367-0.034-0.90.21350.20620.0884-0.6789-0.56170.3844-0.03470.1841-0.0377-0.04650.4230.01680.233-5.878782.0246-14.5063
31.8804-0.1349-0.03072.0125-0.40142.1577-0.0379-0.0725-0.1924-0.1144-0.0605-0.42870.50290.74020.11010.26120.1120.08660.3150.01310.2992-0.916466.4289-29.8465
43.8284-0.7552-0.86123.02471.36051.2038-0.03170.49350.023-0.6533-0.04220.0259-0.1361-0.00810.04910.22580.0376-0.00850.2098-0.00420.1396-15.143375.7134-36.8759
51.21010.9182-0.28461.6288-0.39211.4965-0.06730.03640.0678-0.18270.06380.0723-0.05850.0071-0.00160.16530.0336-0.00280.1331-0.00540.1326-17.005378.2065-31.8621
61.30531.2469-0.94045.059-3.28673.7702-0.0267-0.0683-0.0370.1704-0.0778-0.3428-0.43010.3730.10440.1675-0.0166-0.01270.1970.00040.1685-5.486988.1912-26.8595
71.9144-0.26890.01472.3777-0.84621.9674-0.0650.0391-0.088-0.2094-0.1149-0.4809-0.05650.49950.14870.15890.00880.03640.26960.00710.2202-0.502877.6252-32.6704
85.9095-0.1292.2422.40971.00634.51430.3413-0.4518-0.0771-0.045-0.1524-0.79410.09361.09830.09650.2597-0.00960.07740.57660.04510.4558.076776.0748-36.9157
91.86360.42180.07172.3492-0.22861.725-0.0680.078-0.0678-0.2563-0.0022-0.2418-0.02550.01240.0420.17110.04860.03620.1519-00.171-64.082343.3562-28.0812
100.78240.4289-0.05432.0366-0.59991.2862-0.00050.0839-0.0175-0.2874-0.0811-0.2709-0.10510.08240.04970.19430.0560.04420.1693-0.00230.1713-60.981749.6301-31.5535
113.5801-1.20440.37061.72690.4471.2494-0.16560.0303-0.36490.02570.1330.209-0.1371-0.10040.18840.36770.0113-0.00170.1070.00760.1553-58.530770.3637-53.4142
122.2613-2.49451.01587.6453-3.96523.7789-0.22970.19910.1731-0.56650.2863-0.259-0.18310.35140.02210.4-0.1733-0.05090.30940.00890.2059-39.422278.5624-63.7401
130.7612-0.11570.39170.41010.42990.8395-0.25080.0930.6573-0.0492-0.10350.0974-0.71220.10590.07740.8535-0.0011-0.09690.0837-0.08210.312-44.611193.0799-50.7333
142.0255-0.6201-0.31222.40280.98581.2158-0.1267-0.36250.05720.08120.07810.1223-0.3975-0.18140.08160.4830.0565-0.00490.1229-0.07290.1769-51.641280.7141-45.5644
153.2779-1.0398-0.35561.3147-0.15211.3863-0.1912-0.2375-0.04540.25620.1662-0.0147-0.0974-0.05220.00310.36050.02720.00570.08910.01150.1549-51.362171.8446-45.3545
163.7271-1.62432.3860.783-1.14581.8146-0.0750.14290.09490.0464-0.0263-0.1315-0.21870.27430.11890.3415-0.0785-0.0450.1532-0.00680.1626-36.639474.6929-48.1598
171.9321-0.43210.26430.9613-0.6250.9353-0.406-0.32160.40080.1360.0391-0.2314-0.57520.31760.17050.6393-0.1208-0.12160.1346-0.03970.2555-40.189485.845-45.7698
186.69821.8222-2.66781.5338-0.47695.6033-0.24820.59350.9488-0.11110.3641-0.1341-0.82370.1676-0.14530.8674-0.1638-0.17720.3324-0.05920.4187-37.073394.047-41.6586
193.79462.34310.18774.2798-0.2082.248-0.0652-0.32220.42-0.0743-0.03580.3176-0.20580.23650.14920.14430.0611-0.01610.2101-0.02710.1421-18.990677.2734-9.735
202.4592-2.6636-2.20084.15550.88584.23660.0350.0691-0.2804-0.8253-0.1047-0.01170.7985-0.17140.16850.41040.01010.06060.15950.00390.1909-20.911956.7045-19.8998
210.81910.11-0.30731.2365-0.63721.7767-0.0664-0.3179-0.3242-0.0784-0.182-0.29820.22710.53240.21780.19510.1062-0.0110.43920.10180.2915-7.660960.9631-4.6398
222.00691.15141.50010.6870.85571.2410.5573-1.00420.30770.6001-0.10650.0544-0.2053-0.58960.01370.35520.02080.07110.424-0.05780.2852-27.943870.23283.6153
232.17051.3735-0.08442.3738-0.07941.48160.0771-0.55380.0720.1667-0.12050.0978-0.06280.074-0.01730.14060.04920.00580.31-0.01770.1473-21.292570.2423-1.6352
241.97772.222-1.91712.5562-2.04492.2169-0.0433-0.0817-0.1724-0.0357-0.0058-0.13360.3753-0.0520.04060.21740.0506-0.01010.24710.05340.1486-25.46555.9825-4.4217
250.67820.27770.15431.47710.06971.567-0.0213-0.449-0.4540.1215-0.198-0.39160.62650.35140.1370.36570.12420.01140.43740.18180.3425-12.719252.2533-0.9745
264.13092.15970.90452.1622-0.16542.2511-0.0304-0.03730.377-0.13160.04490.1815-0.3166-0.07610.15060.12920.06140.02230.1871-0.0120.1764-72.852547.3707-9.6511
276.3943-2.0644-2.53365.15830.33885.11440.22220.3966-0.5395-0.2614-0.21550.07050.582-0.4220.02860.1898-0.0548-0.00390.18450.02120.1989-73.832626.3196-19.6732
281.07370.17080.1230.25740.75563.9236-0.029-0.0507-0.30630.06740.1622-0.22680.53280.6625-0.05680.2140.0609-0.0020.26620.04220.4305-58.480224.9158-6.2672
291.3028-0.9738-0.30191.49760.35145.14170.1231-0.2185-0.07160.18860.0532-0.17020.02420.55330.01430.15810.0474-0.04460.1995-0.00020.2598-57.453836.9354-1.6696
303.30951.33841.0572.0197-0.18511.36880.1258-0.38580.20750.322-0.1120.1815-0.0364-0.20750.02820.17640.0388-0.00180.2114-0.01230.1422-73.623736.725-1.2796
312.26031.15980.40272.96310.13081.07150.0445-0.13660.08250.091-0.03750.23740.041-0.2809-0.01930.11030.030.02990.2506-0.02030.1785-78.335238.838-3.3549
321.08520.98730.22161.458-0.13431.14130.03990.00120.05020.10460.02870.10440.1037-0.1328-0.06520.08890.0269-0.0050.1589-0.00360.1675-74.696930.4697-2.1337
331.87780.0475-0.23782.3741-0.51473.0145-0.0564-0.2482-0.44180.2732-0.1626-0.23780.42010.15820.16470.18690.0018-0.02570.18520.04760.292-66.003822.8639-0.4373
341.7310.024-0.44210.7649-0.27590.79330.0687-0.11460.0217-0.0598-0.0163-0.0574-0.21160.08170.03920.3051-0.0355-0.01620.1599-0.00040.1758-50.471769.7034-68.3437
351.36130.9434-0.15766.83720.72160.1342-0.0376-0.18090.13160.34190.21540.05520.0033-0.2442-0.13270.47380.0626-0.0370.27830.04390.2017-68.788579.7028-58.2511
360.976-0.3213-0.75991.78480.19311.08740.00420.07910.4792-0.01520.0011-0.0043-0.6055-0.0964-0.15720.4318-0.0364-0.04530.21280.04270.2765-57.594991.129-73.9501
373.37591.0038-0.26282.1787-0.45651.2439-0.02070.41530.1029-0.109-0.1495-0.06350.1622-0.02510.1140.3124-0.03380.0110.18220.02690.1588-59.922374.3098-76.6328
387.8943-2.27631.16833.96820.18820.25840.02240.9185-0.1108-0.613-0.20160.09850.16430.19620.26190.4012-0.1377-0.01640.2666-0.01090.211-57.206775.0078-84.4415
391.55450.20550.26420.34570.09140.4508-0.07210.1444-0.0834-0.03060.06780.0129-0.0146-0.0070.01360.2986-0.0564-0.00190.16670.00210.1557-60.160971.4537-75.5662
401.42250.29660.7540.29410.46060.6479-0.0574-0.0820.1577-0.17640.01660.0174-0.2459-0.28590.01160.38220.0116-0.01060.1440.02920.1836-70.511379.2846-69.7915
411.9461-0.3821-1.25963.44170.55491.0012-0.10640.25920.1614-0.32720.0490.3866-0.0847-0.1890.17730.3545-0.0311-0.07030.28920.0520.1539-71.202378.2141-82.969
422.20720.39390.68090.81071.29215.4741-0.14250.22370.1608-0.03670.11610.3837-0.5426-0.40010.1040.36840.0773-0.03890.26090.0310.3204-74.126488.3972-74.538
431.4203-0.513-0.45221.8631-0.02251.7384-0.04310.33510.3652-0.256-0.01220.0428-0.2637-0.3115-0.05050.36610.0045-0.06040.26620.07960.2848-65.172789.3739-78.4034
441.0375-0.4535-0.41522.45631.49220.9877-0.22110.03430.6240.12790.17750.1948-0.7026-0.10460.06850.5820.062-0.07680.43330.07760.416-70.061494.537-80.985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 29 through 45 )
2X-RAY DIFFRACTION2chain 'C' and (resid 46 through 59 )
3X-RAY DIFFRACTION3chain 'C' and (resid 60 through 84 )
4X-RAY DIFFRACTION4chain 'C' and (resid 85 through 117 )
5X-RAY DIFFRACTION5chain 'C' and (resid 118 through 188 )
6X-RAY DIFFRACTION6chain 'C' and (resid 189 through 212 )
7X-RAY DIFFRACTION7chain 'C' and (resid 213 through 265 )
8X-RAY DIFFRACTION8chain 'C' and (resid 266 through 281 )
9X-RAY DIFFRACTION9chain 'F' and (resid 29 through 116 )
10X-RAY DIFFRACTION10chain 'F' and (resid 117 through 280 )
11X-RAY DIFFRACTION11chain 'H' and (resid 29 through 45 )
12X-RAY DIFFRACTION12chain 'H' and (resid 46 through 59 )
13X-RAY DIFFRACTION13chain 'H' and (resid 60 through 73 )
14X-RAY DIFFRACTION14chain 'H' and (resid 74 through 103 )
15X-RAY DIFFRACTION15chain 'H' and (resid 107 through 168 )
16X-RAY DIFFRACTION16chain 'H' and (resid 169 through 212 )
17X-RAY DIFFRACTION17chain 'H' and (resid 213 through 265 )
18X-RAY DIFFRACTION18chain 'H' and (resid 266 through 281 )
19X-RAY DIFFRACTION19chain 'J' and (resid 29 through 45 )
20X-RAY DIFFRACTION20chain 'J' and (resid 46 through 59 )
21X-RAY DIFFRACTION21chain 'J' and (resid 60 through 96 )
22X-RAY DIFFRACTION22chain 'J' and (resid 97 through 103 )
23X-RAY DIFFRACTION23chain 'J' and (resid 107 through 168 )
24X-RAY DIFFRACTION24chain 'J' and (resid 169 through 212 )
25X-RAY DIFFRACTION25chain 'J' and (resid 213 through 281 )
26X-RAY DIFFRACTION26chain 'L' and (resid 29 through 45 )
27X-RAY DIFFRACTION27chain 'L' and (resid 46 through 59 )
28X-RAY DIFFRACTION28chain 'L' and (resid 60 through 73 )
29X-RAY DIFFRACTION29chain 'L' and (resid 74 through 84 )
30X-RAY DIFFRACTION30chain 'L' and (resid 85 through 103 )
31X-RAY DIFFRACTION31chain 'L' and (resid 108 through 156 )
32X-RAY DIFFRACTION32chain 'L' and (resid 157 through 212 )
33X-RAY DIFFRACTION33chain 'L' and (resid 213 through 280 )
34X-RAY DIFFRACTION34chain 'D' and (resid 29 through 45 )
35X-RAY DIFFRACTION35chain 'D' and (resid 46 through 59 )
36X-RAY DIFFRACTION36chain 'D' and (resid 60 through 84 )
37X-RAY DIFFRACTION37chain 'D' and (resid 85 through 103 )
38X-RAY DIFFRACTION38chain 'D' and (resid 108 through 116 )
39X-RAY DIFFRACTION39chain 'D' and (resid 117 through 188 )
40X-RAY DIFFRACTION40chain 'D' and (resid 189 through 220 )
41X-RAY DIFFRACTION41chain 'D' and (resid 221 through 231 )
42X-RAY DIFFRACTION42chain 'D' and (resid 232 through 244 )
43X-RAY DIFFRACTION43chain 'D' and (resid 245 through 265 )
44X-RAY DIFFRACTION44chain 'D' and (resid 266 through 281 )

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