[English] 日本語
Yorodumi
- PDB-6mn4: Crystal structure of aminoglycoside acetyltransferase AAC(3)-IVa,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mn4
TitleCrystal structure of aminoglycoside acetyltransferase AAC(3)-IVa, H154A mutant, in complex with apramycin
ComponentsAminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
KeywordsTRANSFERASE/ANTIBIOTIC / ANTIBIOTIC_NAT FAMILY / ACETYLTRANSFERASE / AMINOGLYCOSIDE / ANTIBIOTIC RESISTANCE / COENZYME A / APRAMYCIN / AAC(3)-IVA / CSGID / TRANSFERASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / National Institute of Allergy and Infectious Diseases / NIAID / TRANSFERASE-ANTIBIOTIC complex
Function / homologyaminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / APRAMYCIN / PHOSPHATE ION / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStogios, P.J. / Evdokimova, E. / Michalska, K. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J. / 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)HHSN272201700060C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: Commun Biol / Year: 2022
Title: Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.
Authors: Stogios, P.J. / Bordeleau, E. / Xu, Z. / Skarina, T. / Evdokimova, E. / Chou, S. / Diorio-Toth, L. / D'Souza, A.W. / Patel, S. / Dantas, G. / Wright, G.D. / Savchenko, A.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 6, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 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: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
B: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
C: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
D: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
E: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
F: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,39836
Polymers168,3426
Non-polymers6,05530
Water6,107339
1
A: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2449
Polymers28,0571
Non-polymers1,1878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0576
Polymers28,0571
Non-polymers1,0005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9955
Polymers28,0571
Non-polymers9384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0876
Polymers28,0571
Non-polymers1,0305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0846
Polymers28,0571
Non-polymers1,0275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9304
Polymers28,0571
Non-polymers8733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.550, 130.507, 264.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa


Mass: 28057.070 Da / Num. of mol.: 6 / Mutation: H154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: aacC4, aac(3), aac(3)-IV, aac(3)IV, B9T59_28975, BEN53_26235, BJJ90_27515, BK373_27930, BK400_28640, BVL39_27730, BZL31_07055, BZL69_29365, C5P01_27985, C7235_00480, CR538_26885, CWS33_26775, ...Gene: aacC4, aac(3), aac(3)-IV, aac(3)IV, B9T59_28975, BEN53_26235, BJJ90_27515, BK373_27930, BK400_28640, BVL39_27730, BZL31_07055, BZL69_29365, C5P01_27985, C7235_00480, CR538_26885, CWS33_26775, CXB56_01995, DK267_24825, DK268_23980, DK278_24785, DK279_23955, DK288_24810, DK289_23980, pEC012_00026
Plasmid: pET19bTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold
References: UniProt: Q306W4, aminoglycoside 3-N-acetyltransferase

-
Non-polymers , 7 types, 369 molecules

#2: Chemical
ChemComp-AM2 / APRAMYCIN / NEBRAMYCIN II / 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE / Apramycin


Mass: 539.577 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H41N5O11 / Comment: antibiotic*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7, 30% (w/v) PEG1k, 2.5 mM apramycin

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 66374 / % possible obs: 95.2 % / Redundancy: 9 % / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.063 / Net I/σ(I): 12.77
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.771 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3328 / CC1/2: 0.776 / Rpim(I) all: 0.613 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMA

3sma


Resolution: 2.8→29.327 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.91
RfactorNum. reflection% reflectionSelection details
Rfree0.3043 3627 3 %RANDOM
Rwork0.247 ---
obs0.2487 120976 94.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11627 0 382 339 12348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512308
X-RAY DIFFRACTIONf_angle_d0.97516810
X-RAY DIFFRACTIONf_dihedral_angle_d23.0664477
X-RAY DIFFRACTIONf_chiral_restr0.0521923
X-RAY DIFFRACTIONf_plane_restr0.0062160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83680.39531440.34834573X-RAY DIFFRACTION96
2.8368-2.87560.35061450.33914573X-RAY DIFFRACTION95
2.8756-2.91670.4251350.31754556X-RAY DIFFRACTION97
2.9167-2.96020.33061430.31664586X-RAY DIFFRACTION95
2.9602-3.00640.35941340.31354481X-RAY DIFFRACTION95
3.0064-3.05560.361420.31944557X-RAY DIFFRACTION96
3.0556-3.10830.39011430.30644566X-RAY DIFFRACTION94
3.1083-3.16470.36971450.31654500X-RAY DIFFRACTION96
3.1647-3.22550.33551360.29614481X-RAY DIFFRACTION94
3.2255-3.29130.36631420.29424522X-RAY DIFFRACTION95
3.2913-3.36270.38361390.28644497X-RAY DIFFRACTION93
3.3627-3.44080.39551360.29024473X-RAY DIFFRACTION94
3.4408-3.52680.3661410.28364431X-RAY DIFFRACTION92
3.5268-3.62190.32291330.27454449X-RAY DIFFRACTION94
3.6219-3.72830.29951360.25974412X-RAY DIFFRACTION92
3.7283-3.84840.28331390.24154355X-RAY DIFFRACTION92
3.8484-3.98560.35121370.24574396X-RAY DIFFRACTION92
3.9856-4.14480.28471340.23824299X-RAY DIFFRACTION91
4.1448-4.33290.28531420.22764390X-RAY DIFFRACTION91
4.3329-4.56050.27381360.21484370X-RAY DIFFRACTION92
4.5605-4.8450.28041330.20714480X-RAY DIFFRACTION94
4.845-5.21720.26381360.2024565X-RAY DIFFRACTION96
5.2172-5.73870.26671510.22034671X-RAY DIFFRACTION99
5.7387-6.5610.25831460.22794788X-RAY DIFFRACTION99
6.561-8.23570.24051370.21284743X-RAY DIFFRACTION100
8.2357-29.32880.26211420.20474635X-RAY DIFFRACTION97
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)
12.42551.0974-0.82923.0185-1.10062.595-0.01790.005-0.22180.03170.01360.0696-0.18950.16870.03820.2065-0.0226-0.01140.6827-0.02780.41-28.927324.0962-16.3654
24.7814-2.68310.10215.3958-2.09341.29710.0929-0.9053-0.24290.0938-0.2537-0.15050.03440.01530.13180.2659-0.0284-0.02270.88620.02640.435-27.970519.125-3.8317
35.5938-1.94172.59793.63360.74392.130.2297-1.2243-0.35720.87090.20320.47250.2078-0.9825-0.33390.2870.02360.17270.87630.04830.4951-40.705120.2457-2.6168
43.4098-0.51151.5285.5697-2.48022.959-0.3531-0.2534-0.85840.4828-0.02930.0318-0.2032-0.06260.36710.28810.00520.00770.73470.02660.6554-44.45369.9079-6.1022
51.8390.7575-0.97434.44270.99885.39410.2302-0.9065-0.44840.6388-0.0511-0.1902-0.719-0.53110.0410.59610.15010.08090.78640.22480.8638-37.39294.03782.7614
63.42123.3646-2.81057.2152-3.76182.5314-0.06830.18210.4021-0.40380.16331.3455-0.029-0.2163-0.07320.3029-0.0574-0.07350.7989-0.08350.4853-46.734719.3273-21.6199
78.05842.0665-1.62026.6759-2.51773.10570.0333-0.0115-0.6024-0.10030.04850.65380.3051-0.1631-0.03270.21790.0201-0.01290.51340.02070.4634-50.44069.9447-13.4798
83.26391.67581.64914.1967-0.40446.5173-0.0544-0.18060.27340.34980.31490.3249-0.4126-0.6143-0.23440.26350.05690.00330.73150.04320.4151-7.037521.41873.6412
97.30610.19934.35533.0143-0.0763.23150.10760.6242-0.4525-0.1712-0.0225-0.36460.04360.1953-0.07120.25170.02840.02440.5813-0.04760.3994-6.314.2992-14.3121
104.79611.4899-0.83583.12052.61413.7151-0.2020.245-0.7549-0.3321-0.22020.20260.135-0.39280.42110.34550.1059-0.050.5039-0.02340.719-2.12490.7843-17.0012
112.6942-1.36830.04976.23453.33724.7645-0.0403-0.4733-1.02450.42250.1557-0.23970.53430.4719-0.13380.34040.0155-0.01740.49810.14290.77287.33181.7778-2.7128
125.323-3.0973-3.08316.70323.97878.25720.23320.09440.1861-0.33710.23770.01950.1807-0.5796-0.44290.2729-0.0352-0.06510.73190.18360.3717-3.340117.368722.5243
132.38851.1735-1.23966.4899-2.27515.23130.0701-0.3040.12360.37760.08310.47050.2027-0.1884-0.1580.40570.117-0.00990.83390.09740.3877-6.10211.865139.0644
147.33411.4436-3.62264.5571-0.79782.37070.3446-0.1910.49150.4889-0.03190.6258-0.7381-1.0847-0.33770.51310.10080.16840.98030.10310.5889-14.855422.41841.2338
157.8681-0.9631-1.73523.29381.572.7122-0.07290.2861-1.16630.3238-0.22490.71980.1997-0.55840.3310.76650.03550.46531.49350.29310.8855-24.588312.086348.9999
166.5731-0.598-4.02484.91710.72762.45410.35960.37951.3461-0.31750.2770.8529-0.3252-0.8024-0.55670.56110.27190.13521.27740.26320.8097-17.965228.804229.0704
175.24793.9122.29574.3929-0.05354.25080.46780.2151-0.91580.1110.2009-0.1571-0.2389-0.6297-0.66610.51930.09430.10991.68030.37581.3679-35.541221.617936.8698
180.91660.04620.32358.6933-0.60764.62580.16180.3058-0.076-0.026-0.1557-0.00610.0486-0.5301-0.03430.3392-0.05120.01880.8443-0.06980.3404-33.078526.408-41.4738
193.3764-0.0069-2.01073.11042.78446.1364-0.24150.8223-0.3327-0.85610.2772-0.3605-0.59550.2638-0.00570.5923-0.14780.11410.8755-0.11750.4429-25.603823.5362-58.9902
201.99291.03240.48480.8265-0.35471.4098-0.25750.1548-0.9015-0.55620.5769-0.96980.65251.20860.04880.8514-0.23670.39821.5185-0.50781.0698-11.701420.193-60.9312
211.6833-0.3319-1.3853.99890.1111.1417-0.50020.0332-0.1170.33160.5924-1.48690.04120.4285-0.29250.475-0.15810.00531.2864-0.1550.69-13.886731.5573-40.7848
226.8147-0.2928-3.01540.57511.18833.38620.05540.2851-0.1772-0.28750.8142-1.1334-0.10881.5553-0.77930.6685-0.1810.16031.4013-0.48261.0681-5.608226.8348-49.4536
232.14630.455-0.48043.38763.06446.1231-0.24970.2746-0.1750.1624-0.74280.56920.856-1.67840.58550.8415-0.2620.24961.1598-0.4870.7777-44.3168.7917-57.2996
241.73610.57151.08141.83190.62421.50250.1694-0.0023-0.9250.8426-0.36460.31171.9507-1.07010.15982.1974-0.64830.46791.2231-0.40351.2106-46.1342-9.9129-54.1263
252.7346-1.94-0.03437.5386-3.37058.02370.14310.2103-0.2233-1.348-1.3564-0.7691.97332.35740.4971.03910.2620.19961.16240.46480.76842.1344-5.381737.5297
261.61230.08550.11052.2465-0.05950.23260.20490.0952-1.4603-1.593-0.51960.57152.55860.27070.08553.23210.3690.00791.14340.28951.397-4.1342-21.725333.9281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 172 )
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 190 )
6X-RAY DIFFRACTION6chain 'A' and (resid 191 through 213 )
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 257 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 52 )
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 143 )
10X-RAY DIFFRACTION10chain 'B' and (resid 144 through 190 )
11X-RAY DIFFRACTION11chain 'B' and (resid 191 through 257 )
12X-RAY DIFFRACTION12chain 'C' and (resid 0 through 39 )
13X-RAY DIFFRACTION13chain 'C' and (resid 40 through 114 )
14X-RAY DIFFRACTION14chain 'C' and (resid 115 through 159 )
15X-RAY DIFFRACTION15chain 'C' and (resid 160 through 190 )
16X-RAY DIFFRACTION16chain 'C' and (resid 191 through 232 )
17X-RAY DIFFRACTION17chain 'C' and (resid 233 through 257 )
18X-RAY DIFFRACTION18chain 'D' and (resid 0 through 52 )
19X-RAY DIFFRACTION19chain 'D' and (resid 53 through 143 )
20X-RAY DIFFRACTION20chain 'D' and (resid 144 through 190 )
21X-RAY DIFFRACTION21chain 'D' and (resid 191 through 213 )
22X-RAY DIFFRACTION22chain 'D' and (resid 214 through 257 )
23X-RAY DIFFRACTION23chain 'E' and (resid 0 through 114 )
24X-RAY DIFFRACTION24chain 'E' and (resid 115 through 257 )
25X-RAY DIFFRACTION25chain 'F' and (resid 0 through 103 )
26X-RAY DIFFRACTION26chain 'F' and (resid 104 through 250 )

+
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