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- PDB-12ss: Crystal Structure of Superoxide dismutase from Cryptosporidium parvum -

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Basic information

Entry
Database: PDB / ID: 12ss
TitleCrystal Structure of Superoxide dismutase from Cryptosporidium parvum
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Superoxide dismutase / Cryptosporidium parvum
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Superoxide dismutase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Superoxide dismutase from Cryptosporidium parvum
Authors: Liu, L. / Ung, A.R. / Lovell, S. / Cooper, A. / Battaile, K.P.
History
DepositionApr 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
E: Superoxide dismutase
F: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,79414
Polymers141,2966
Non-polymers4988
Water4,378243
1
A: Superoxide dismutase
hetero molecules

C: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2094
Polymers47,0992
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+1/31
Buried area1890 Å2
ΔGint-10 kcal/mol
Surface area16350 Å2
MethodPISA
2
B: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3776
Polymers47,0992
Non-polymers2784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-4 kcal/mol
Surface area16490 Å2
MethodPISA
3
E: Superoxide dismutase
F: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2094
Polymers47,0992
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-8 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.805, 92.805, 125.765
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Superoxide dismutase


Mass: 23549.318 Da / Num. of mol.: 6 / Fragment: P26-S221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd5_3230 / Plasmid: CrpaA.01199.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3FQJ9
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Berkeley D6: 25% (w/v) PEG 3350, 100 mM MES pH 5.5, 200 mM Ammonium acetate. ChtrB.20815.a.B1.PW39484 at 13.5 mg/mL. Metal assigned as Mn acquired from expression. P31 twinned, plate 20585 ...Details: Berkeley D6: 25% (w/v) PEG 3350, 100 mM MES pH 5.5, 200 mM Ammonium acetate. ChtrB.20815.a.B1.PW39484 at 13.5 mg/mL. Metal assigned as Mn acquired from expression. P31 twinned, plate 20585 D6 drop1, Puck: PSL-2101, Cryo: 20% PEG 200 + 80% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jan 31, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.01→46.4 Å / Num. obs: 161236 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.04 / Rrim(I) all: 0.132 / Χ2: 1.07 / Net I/σ(I): 14.8
Reflection shellResolution: 2.01→2.06 Å / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 1.437 / Num. measured all: 65931 / Num. unique obs: 6024 / CC1/2: 0.552 / Rpim(I) all: 0.454 / Rrim(I) all: 1.507 / Χ2: 0.91 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(2.1rc1_6025: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→46.4 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.56 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1965 7734 4.8 %
Rwork0.1486 --
obs0.1562 161236 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 17 243 9612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119708
X-RAY DIFFRACTIONf_angle_d0.72713204
X-RAY DIFFRACTIONf_dihedral_angle_d15.3173387
X-RAY DIFFRACTIONf_chiral_restr0.0451401
X-RAY DIFFRACTIONf_plane_restr0.0061687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.020.3551640.26192690X-RAY DIFFRACTION94
2.02-2.030.30591320.24462772X-RAY DIFFRACTION95
2.03-2.050.22531120.23982732X-RAY DIFFRACTION96
2.05-2.060.28141480.25413066X-RAY DIFFRACTION95
2.06-2.070.2861800.24262672X-RAY DIFFRACTION94
2.08-2.090.29691280.24722708X-RAY DIFFRACTION95
2.09-2.10.28461480.23522898X-RAY DIFFRACTION95
2.1-2.120.26081400.23512768X-RAY DIFFRACTION95
2.12-2.130.2282960.22532744X-RAY DIFFRACTION97
2.13-2.150.23041200.2242860X-RAY DIFFRACTION96
2.15-2.170.2746920.21262816X-RAY DIFFRACTION97
2.17-2.180.22262360.22678X-RAY DIFFRACTION92
2.18-2.20.23151520.20472848X-RAY DIFFRACTION95
2.2-2.220.22092040.212720X-RAY DIFFRACTION93
2.22-2.240.21031800.20622718X-RAY DIFFRACTION94
2.24-2.250.21341160.20432804X-RAY DIFFRACTION96
2.25-2.270.241280.20222876X-RAY DIFFRACTION96
2.27-2.290.23351120.19922784X-RAY DIFFRACTION96
2.29-2.310.27511840.19172770X-RAY DIFFRACTION94
2.32-2.340.27281480.1942844X-RAY DIFFRACTION95
2.34-2.360.21312000.19182676X-RAY DIFFRACTION93
2.36-2.380.19761160.18612770X-RAY DIFFRACTION96
2.38-2.410.19891600.18242792X-RAY DIFFRACTION95
2.41-2.430.29021040.18162888X-RAY DIFFRACTION97
2.43-2.460.23951600.17642752X-RAY DIFFRACTION95
2.46-2.490.17781160.17462758X-RAY DIFFRACTION96
2.49-2.520.22141480.17872858X-RAY DIFFRACTION95
2.52-2.550.23681760.16082708X-RAY DIFFRACTION94
2.55-2.580.17621280.16352862X-RAY DIFFRACTION96
2.58-2.610.1871000.1712770X-RAY DIFFRACTION97
2.61-2.650.25871720.17082834X-RAY DIFFRACTION94
2.65-2.690.20131680.16812650X-RAY DIFFRACTION94
2.69-2.730.18871320.16282908X-RAY DIFFRACTION96
2.73-2.770.17331400.15242738X-RAY DIFFRACTION95
2.77-2.820.20311280.14592818X-RAY DIFFRACTION96
2.82-2.860.16091120.14412764X-RAY DIFFRACTION96
2.86-2.920.19691520.14392808X-RAY DIFFRACTION95
2.92-2.970.20061560.14482768X-RAY DIFFRACTION95
2.97-3.030.1987920.15212832X-RAY DIFFRACTION97
3.03-3.10.2104940.15332842X-RAY DIFFRACTION97
3.1-3.170.23041760.15182752X-RAY DIFFRACTION94
3.17-3.250.2226960.15692872X-RAY DIFFRACTION97
3.25-3.340.1891560.14722750X-RAY DIFFRACTION95
3.34-3.440.17281320.15532846X-RAY DIFFRACTION96
3.44-3.550.21411640.14612752X-RAY DIFFRACTION94
3.55-3.670.17861480.14712770X-RAY DIFFRACTION95
3.67-3.820.22991160.14392818X-RAY DIFFRACTION96
3.82-3.990.23041560.1342802X-RAY DIFFRACTION95
4-4.20.18071520.12192724X-RAY DIFFRACTION95
4.21-4.470.1961840.11362902X-RAY DIFFRACTION97
4.47-4.810.11621440.10362750X-RAY DIFFRACTION95
4.81-5.30.1507440.10882858X-RAY DIFFRACTION98
5.3-6.060.19371420.12582814X-RAY DIFFRACTION95
6.06-7.630.16581880.14172774X-RAY DIFFRACTION94
7.64-46.40.19571620.1472754X-RAY DIFFRACTION94
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)
11.53910.4338-0.42140.56390.16421.5064-0.0573-0.2649-0.12630.20460.1152-0.17920.03780.2512-0.060.22340.0652-0.01750.3168-0.00710.298534.2527-1.42348.6119
26.52820.9533.38864.94311.46284.21360.1502-0.2896-0.84670.17310.0878-0.02540.6368-0.1295-0.21150.32960.03540.04820.25490.03180.314921.6694-18.09347.7345
30.5121-0.0823-0.41982.23270.21672.0772-0.0367-0.0482-0.13970.1069-0.01390.06220.18150.19480.04710.23740.0337-0.00490.2451-0.01550.263623.5343-8.22973.7184
48.4149-2.28223.61161.8397-1.70186.16150.10820.7090.2127-0.3774-0.1095-0.2003-0.12950.37950.02380.3052-0.01990.03980.29110.01480.221229.3855.9455-13.625
50.90660.1618-1.270.4348-0.43793.8090.06070.18510.20260.1548-0.00210.003-0.3734-0.2612-0.06230.2120.0315-0.0280.2391-0.00010.272718.70285.6916-4.577
61.20491.10170.09991.4067-0.13084.1223-0.03340.1697-0.0358-0.14280.08160.13330.0555-0.1582-0.04310.18870.0202-0.02190.2556-0.00510.268416.0041-5.0019-8.7407
70.7754-0.3685-1.16181.02370.1971.87510.07760.02090.19120.00860.0052-0.0282-0.3068-0.0242-0.07370.22740.0281-0.01690.2533-0.00610.278124.31557.17874.1404
86.4412.51692.94389.5598-1.70962.4540.01780.7423-0.3391-0.08330.3136-0.59450.13450.6476-0.32830.241-0.00490.03770.3182-0.03520.243331.1883-2.4083-10.7446
90.3385-0.0565-0.29232.13570.48732.22180.0285-0.0621-0.1590.299-0.09780.24970.6774-0.4030.05140.3894-0.10160.02440.2355-0.02030.27554.263126.0538-13.7288
102.5850.6544-0.08483.6778-0.36385.68070.00920.21440.0126-0.29580.0222-0.34010.07990.5444-0.04860.17370.00120.03160.22530.01420.218519.587934.6305-32.0563
110.81550.10730.28110.93730.7143.0074-0.01980.03420.0591-0.0292-0.004-0.0082-0.0508-0.09810.02090.21460.0099-0.00110.1660.00430.245511.349937.0878-22.2645
127.084-4.75224.34288.9892-1.65378.83480.46670.2949-0.6931-0.3307-0.00970.21350.80950.1344-0.41110.24910.02790.04160.1845-0.01120.181113.779125.3639-30.7391
131.80630.05981.00421.2741-0.01022.34810.0013-0.00980.0371-0.02550.0241-0.1297-0.0710.2273-0.02180.1603-0.0238-0.03610.2742-0.01360.2597.6017-10.5526-21.6
142.3287-0.8723-1.21541.59220.18145.2636-0.188-0.44080.26490.224-0.0275-0.0066-0.2897-0.22870.23070.2110.0445-0.0780.3421-0.06030.3189-5.7486-1.7418-17.3619
152.33390.9631.57641.49240.73412.4921-0.0224-0.33740.1960.1884-0.07260.0202-0.0147-0.20740.09480.21180.0058-0.01590.3066-0.04110.2441-1.6484-10.2009-18.1126
161.9127-0.24150.73923.0896-0.0955.97980.08170.0331-0.03820.21580.2076-0.3719-0.10040.4071-0.25630.2451-0.0340.01090.2435-0.09340.315220.634151.1354-1.2192
172.25850.87290.26660.4268-0.44453.41230.13740.25330.6524-1.1582-0.2081-0.0101-0.56920.1157-0.02720.77740.00310.050.26560.04350.429211.452765.8498-13.3539
182.4214-0.46350.91894.08323.12623.2904-0.071-0.04830.1889-0.1493-0.01810.1175-0.158-0.01520.08210.2602-0.01920.02720.1909-0.01050.246511.315655.1124-4.4519
197.4681.18020.05151.07511.64823.02690.5286-0.65580.15070.5212-0.36750.36430.3742-0.3807-0.13320.5708-0.10320.17240.2907-0.00820.34391.50550.404615.886
201.7371-0.5717-0.9370.23040.64983.4991-0.0679-0.1776-0.21440.3453-0.2930.27040.5449-0.47050.34940.3256-0.10320.09780.2614-0.05450.37950.122944.93352.6953
216.0023-2.9917-4.28832.74910.37725.57840.1042-0.04810.27110.1999-0.12470.6987-0.4706-0.26010.03960.2444-0.02190.06910.253-0.07470.4623-5.808254.79322.2317
221.6136-0.1327-0.88022.24441.99073.43550.0489-0.03930.06560.2854-0.1690.26450.2379-0.16980.10310.2157-0.04230.0390.1593-0.01810.22037.544746.6815-2.2761
231.1628-0.769-0.46094.10413.83025.3406-0.05150.0253-0.04920.4512-0.03740.12690.5063-0.25960.09380.3566-0.04520.07830.2229-0.02050.2247.012148.41619.6607
243.9097-0.6544-1.56373.64160.50624.7959-0.0117-0.1918-0.26610.67520.0263-0.16730.26080.272-0.01640.34680.0584-0.04170.2226-0.01880.2892-23.43762.6193-14.2794
256.4223-0.5316-2.13431.2246-1.19242.5751-0.25550.2295-0.30740.09260.1270.27620.3468-0.27990.10810.3485-0.03480.03940.293-0.07790.3761-40.81432.0352-17.7535
269.0786-2.09914.55772.46390.20758.17340.13991.48920.0374-0.25960.0998-0.3884-0.53691.2612-0.21210.3625-0.06710.09170.5312-0.05830.4183-15.72388.5358-30.0092
272.13990.6914-0.23272.79891.25384.4920.0010.37010.1399-0.35390.0503-0.2099-0.33590.1464-0.05270.21150.01580.00090.27380.02630.2594-28.220317.4205-32.512
282.91740.43811.3051.651-0.42914.73080.04370.2412-0.0412-0.301-0.1470.07370.2091-0.02380.11890.31520.0589-0.020.3318-0.03160.3459-37.75513.2161-31.0882
291.3532-1.8603-2.18613.92722.80925.98430.17160.1110.029-0.1622-0.1263-0.1672-0.2359-0.0026-0.06220.20530.01910.0010.25390.01370.285-24.404512.7689-22.5435
302.719-1.47480.27664.86030.65323.09370.01960.10120.0421-0.0311-0.0314-0.0573-0.4224-0.08850.05190.4185-0.02560.04340.2592-0.04420.3088-32.545833.8705-6.8767
313.4892-0.9126-2.26922.37530.60062.1199-0.3619-0.3693-0.2220.77850.03990.59230.6164-0.39240.29830.7529-0.09580.16870.406-0.01260.4289-44.905320.40269.6082
321.3694-1.021-0.15692.91040.89133.2493-0.0844-0.1286-0.12350.4981-0.07090.50240.1988-0.35770.15440.3484-0.05240.07870.2556-0.04910.3486-41.336223.3079-0.6685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 180 )
7X-RAY DIFFRACTION7chain 'A' and (resid 181 through 210 )
8X-RAY DIFFRACTION8chain 'A' and (resid 211 through 221 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 105 )
10X-RAY DIFFRACTION10chain 'B' and (resid 106 through 143 )
11X-RAY DIFFRACTION11chain 'B' and (resid 144 through 209 )
12X-RAY DIFFRACTION12chain 'B' and (resid 210 through 221 )
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 129 )
14X-RAY DIFFRACTION14chain 'C' and (resid 130 through 168 )
15X-RAY DIFFRACTION15chain 'C' and (resid 169 through 220 )
16X-RAY DIFFRACTION16chain 'D' and (resid 26 through 66 )
17X-RAY DIFFRACTION17chain 'D' and (resid 67 through 87 )
18X-RAY DIFFRACTION18chain 'D' and (resid 88 through 105 )
19X-RAY DIFFRACTION19chain 'D' and (resid 106 through 129 )
20X-RAY DIFFRACTION20chain 'D' and (resid 130 through 154 )
21X-RAY DIFFRACTION21chain 'D' and (resid 155 through 168 )
22X-RAY DIFFRACTION22chain 'D' and (resid 169 through 199 )
23X-RAY DIFFRACTION23chain 'D' and (resid 200 through 220 )
24X-RAY DIFFRACTION24chain 'E' and (resid 26 through 54 )
25X-RAY DIFFRACTION25chain 'E' and (resid 55 through 105 )
26X-RAY DIFFRACTION26chain 'E' and (resid 106 through 116 )
27X-RAY DIFFRACTION27chain 'E' and (resid 117 through 157 )
28X-RAY DIFFRACTION28chain 'E' and (resid 158 through 180 )
29X-RAY DIFFRACTION29chain 'E' and (resid 181 through 221 )
30X-RAY DIFFRACTION30chain 'F' and (resid 26 through 104 )
31X-RAY DIFFRACTION31chain 'F' and (resid 105 through 143 )
32X-RAY DIFFRACTION32chain 'F' and (resid 144 through 220 )

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