[English] 日本語
Yorodumi
- PDB-4ivf: Crystal structure of glutathione transferase homolog from Loddero... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ivf
TitleCrystal structure of glutathione transferase homolog from Lodderomyces elongisporus, target EFI-501753, with two GSH per subunit
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / GST / glutathione S-transferase / Enzyme Function Initiative / EFI / Structural Genomics
Function / homology
Function and homology information


Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / GLUTATHIONE / Uncharacterized protein
Similarity search - Component
Biological speciesLodderomyces elongisporus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of glutathione transferase homolog from Lodderomyces elongisporus, target EFI-501753, with two GSH per subunit
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionJan 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Putative uncharacterized protein
G: Putative uncharacterized protein
H: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,01525
Polymers211,9068
Non-polymers5,10917
Water22,8971271
1
A: Putative uncharacterized protein
F: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2066
Polymers52,9762
Non-polymers1,2294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-35 kcal/mol
Surface area18390 Å2
MethodPISA
2
B: Putative uncharacterized protein
G: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2066
Polymers52,9762
Non-polymers1,2294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-34 kcal/mol
Surface area18080 Å2
MethodPISA
3
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2066
Polymers52,9762
Non-polymers1,2294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-34 kcal/mol
Surface area17900 Å2
MethodPISA
4
E: Putative uncharacterized protein
H: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3987
Polymers52,9762
Non-polymers1,4215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-33 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.598, 112.476, 194.384
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Putative uncharacterized protein


Mass: 26488.191 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lodderomyces elongisporus (fungus) / Strain: NRRL YB-4239 / Gene: LELG_04376 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5E437
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1271 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.17M Amm Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5% Peg4000, 15% (V/V) glycerol); Cryoprotection (Reservoir taken to 20% glycerol), ...Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.17M Amm Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5% Peg4000, 15% (V/V) glycerol); Cryoprotection (Reservoir taken to 20% glycerol), vapor diffusion, sitting drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 16, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→194.384 Å / Num. all: 99618 / Num. obs: 99618 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rsym value: 0.175 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.326.10.71.187431142860.797.9
2.32-2.466.10.5431.482620135200.54398
2.46-2.6360.4151.877366128050.41598.3
2.63-2.8460.2962.571652119200.29698.3
2.84-3.1160.2143.465824110350.21498.6
3.11-3.4860.1544.559681100250.15498.7
3.48-4.0260.1314.85364689270.13199
4.02-4.926.20.1195.14728576240.11999.5
4.92-6.966.70.0926.44075660540.092100
6.96-40.0226.70.057102282734220.05798.6

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GX0
Resolution: 2.2→37.126 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8365 / SU ML: 0.26 / σ(F): 0 / σ(I): 0 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 4984 5.01 %RANDOM
Rwork0.1559 ---
obs0.1592 99532 98.2 %-
all-99532 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.71 Å2 / Biso mean: 24.4895 Å2 / Biso min: 2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14481 0 333 1271 16085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715197
X-RAY DIFFRACTIONf_angle_d1.01820619
X-RAY DIFFRACTIONf_chiral_restr0.0752185
X-RAY DIFFRACTIONf_plane_restr0.0052655
X-RAY DIFFRACTIONf_dihedral_angle_d13.6365587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.30111540.21233082323697
2.225-2.25120.30671560.22563111326798
2.2512-2.27860.28581750.21183046322198
2.2786-2.30750.321790.20213107328698
2.3075-2.33780.27141640.20413091325597
2.3378-2.36980.27741570.18963129328698
2.3698-2.40370.2941580.19753086324497
2.4037-2.43960.27521870.2053111329898
2.4396-2.47770.29191780.19713062324098
2.4777-2.51830.29391470.19633139328698
2.5183-2.56170.27471840.193088327298
2.5617-2.60830.27531830.1783116329998
2.6083-2.65840.26121660.17683110327698
2.6584-2.71270.2351640.1693111327598
2.7127-2.77160.28331480.16573147329598
2.7716-2.83610.2551660.16363112327898
2.8361-2.9070.2331690.16333128329798
2.907-2.98560.27671650.16443156332198
2.9856-3.07340.23231400.16633148328898
3.0734-3.17250.25371550.16133145330098
3.1725-3.28580.22911690.15383176334598
3.2858-3.41730.20181700.14233167333798
3.4173-3.57270.17322030.12943122332599
3.5727-3.76090.16791660.12353183334998
3.7609-3.99630.18021840.12533156334099
3.9963-4.30440.17771610.12273241340299
4.3044-4.73680.16931470.11923254340199
4.7368-5.42040.17321540.123532723426100
5.4204-6.82220.22691430.149433463489100
6.8222-37.13110.17771920.16193406359899
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)
12.70630.15540.39751.820.17372.63370.11510.06290.1818-0.1591-0.00610.0623-0.1699-0.1359-0.06860.09140.00980.01480.19060.03370.11993.330695.224168.3915
26.15252.41811.96258.58861.97275.5003-0.1506-0.16520.50670.58370.0330.2519-0.3285-0.14940.09610.14850.0357-0.0060.2274-0.01870.1417-3.816495.964783.859
30.9939-0.3938-0.4321.407-0.15091.39140.02980.4522-0.0417-0.0547-0.05250.11660.0363-0.49810.02210.10210.00750.01580.28080.00130.10920.051585.504370.9047
42.8819-0.4553-0.99694.2780.6982.64890.04520.76950.0057-0.5501-0.0571-0.09430.2702-0.2029-0.0080.1721-0.02590.03850.4374-0.0740.092613.056580.649258.5985
50.41230.08030.55774.15612.41853.8229-0.05910.1816-0.1786-0.0839-0.1179-0.07980.02710.00240.10860.1084-0.00520.03170.2537-0.06970.058917.827679.63471.6484
62.89430.44450.26954.09061.84247.5422-0.118-0.23980.28530.1461-0.07740.1816-0.3006-0.05720.20940.0663-0.0006-0.0170.1327-0.01180.169816.974696.349890.077
70.8825-0.1091-0.33660.88170.47433.49180.0151-0.10260.05490.0397-0.0196-0.21110.12610.2083-0.04640.077-0.0194-0.02620.11040.0020.163926.436589.679982.9498
84.3567-0.7810.89281.74330.98461.70150.250.45490.2695-0.32790.1886-0.3975-0.1510.1604-0.35810.1847-0.04630.08780.3307-0.00940.202225.477185.757762.093
94.421.54741.97331.50140.07043.1572-0.1655-0.05410.2871-0.14530.1037-0.0019-0.4263-0.27720.03580.08570.0302-0.01650.13210.02630.183417.86795.888875.0205
103.6077-0.5811.68021.23720.40423.8974-0.07820.1120.1823-0.10580.0431-0.2462-0.40170.16410.04910.0833-0.01570.00410.13040.05160.226126.794197.513571.0937
115.33172.2562-4.32522.3132-0.45494.92430.70350.11041.0828-0.0897-0.48630.0269-0.9094-0.2229-0.65380.2368-0.0080.01090.30110.0760.26729.801103.248468.0962
121.9093-1.1185-0.93171.35710.27810.58330.0469-0.17551.1120.11250.1214-0.511-0.34240.20620.14530.228-0.052-0.00210.0950.07070.725259.085568.598367.2
132.5427-1.68722.25441.3767-1.50663.5449-0.0604-0.01740.7153-0.080.30750.2666-0.3245-0.3865-0.16170.1840.00810.02790.25440.11510.498648.473665.18961.5759
142.7668-0.44071.20380.7141-0.29332.1288-0.02090.25420.297-0.0455-0.0529-0.1006-0.01280.2770.08270.11360.00390.00590.16010.03780.17462.800948.256361.9152
152.7601-0.92450.24271.9335-0.59791.98990.03680.3260.5780.0145-0.0237-0.5015-0.27560.5525-0.00790.1553-0.04920.01050.27590.03140.291171.424651.678858.7061
162.82440.1824-1.56790.29320.01654.16110.119-0.08340.8597-0.0918-0.1783-0.1005-0.60180.5195-0.27980.262-0.13970.04760.35370.2270.700769.147165.247754.9346
172.43180.5420.15892.4883-0.09921.40640.00910.0547-0.7107-0.03550.0457-0.2430.31180.0634-0.0420.21120.03550.02270.2066-0.02370.324118.043613.380878.2578
181.90860.51540.09171.05370.21741.76250.0779-0.1374-0.31020.1052-0.02930.01110.2502-0.2425-0.04780.1773-0.02930.01620.20580.06280.21720.774120.535388.0043
190.12640.31340.42281.83812.06363.20440.423-0.5591-0.67140.51110.0907-0.40750.4360.2633-0.37570.4454-0.0269-0.00250.3580.1410.493513.38917.558293.2376
201.3708-0.2909-0.40891.5645-0.34652.2751-0.05150.02890.0451-0.04110.03910.06930.0366-0.29620.01390.098-0.0005-0.01290.28490.02270.179-3.89636.741373.3686
215.151.613-0.94333.01421.50891.6699-0.08680.61610.0562-0.5027-0.02810.22630.1024-0.37810.08140.2225-0.0538-0.01690.3568-0.10960.18748.966527.270658.7792
221.93620.0672-0.25861.38760.10522.68630.0227-0.0675-0.12930.061-0.0851-0.09730.09750.01620.07830.0777-0.0131-0.00890.11870.03640.146417.607733.608978.9277
233.17510.13031.43550.8411-0.6862.1406-0.09840.05050.5080.00130.0290.1165-0.256-0.04850.06720.14480.03850.01720.13570.00760.21415.398643.821772.8993
242.17750.1250.05760.97140.14442.0905-0.0188-0.0493-0.2244-0.02360.0039-0.01830.1566-0.03170.00220.0971-0.00010.01840.05350.01750.090638.176933.285331.6331
250.59751.0247-0.41872.66751.72586.8727-0.0157-0.1682-0.15710.30230.0633-0.7476-0.38660.82920.06210.179-0.0458-0.09980.22820.0630.269551.878149.712634.7142
262.49890.77032.15151.00831.05253.3958-0.08850.1045-0.00120.04550.0219-0.0506-0.1711-0.12260.06280.11770.02150.00110.11840.0280.099930.796948.235222.0511
270.9613-0.38340.78240.73-0.03571.4214-0.09920.23890.1386-0.1525-0.0114-0.0878-0.15310.19220.07290.1637-0.0257-0.00270.18470.05670.097939.404947.824115.9654
281.39490.31650.11192.1238-0.10421.6174-0.01030.1663-0.2461-0.04130.0613-0.21560.23850.1252-0.0550.13650.0285-0.01130.1904-0.0590.133122.328368.24579.0563
293.4052-0.85050.34780.2315-0.47957.22950.02270.6302-0.7319-0.31680.0210.18620.49370.0099-0.05950.2102-0.0576-0.0380.2779-0.1260.25242.33265.870970.8919
301.4180.3360.69211.42740.56051.81130.0113-0.01650.01580.09360.01660.10780.1503-0.1029-0.03530.1042-0.01060.02660.1383-0.0140.07816.555378.712189.0636
312.3338-0.88140.01740.9274-0.03050.93650.0272-0.3947-0.27920.01360.09510.10040.18470.0559-0.13680.2134-0.03030.00850.1820.03650.14599.140567.196995.1479
323.104-0.1009-0.37621.62980.13691.72-0.11080.0366-0.40840.10740.0443-0.01350.27910.1130.03010.14410.00590.00170.13110.0150.103649.182434.163368.2077
331.92410.37121.26440.9527-0.12172.3130.02720.11850.0111-0.0114-0.0506-0.09320.0529-0.0292-0.00840.09380.00510.01880.11440.02640.078144.511141.781459.1321
341.998-0.06290.28284.1252-0.5817.1502-0.17080.21960.1614-0.5666-0.17380.5976-0.0062-0.17340.16970.15840.0226-0.00370.26680.03630.176734.644353.561764.5191
351.8236-0.22390.37290.9757-1.73414.06260.2619-0.13630.49350.01280.1673-0.1048-0.2707-0.2736-0.34180.16540.01460.0130.0938-0.00820.235747.234756.907669.174
366.0636-1.76332.66134.2136-1.89945.1829-0.1538-0.57580.08370.18720.0592-0.057-0.01660.0260.03910.11450.03190.01420.2084-0.04640.175762.657643.908283.5402
373.3859-0.46111.73950.4353-0.6641.4172-0.0943-0.34450.47940.13350.1425-0.1934-0.13310.08340.02910.14950.0311-0.04420.2712-0.11840.19148.605456.785981.5267
381.21880.4516-0.28152.20080.96621.9106-0.0295-0.42210.01170.19070.0732-0.10110.0488-0.0772-0.04790.15320.0501-0.00660.2021-0.03830.101345.354348.701285.0981
394.6182-0.53472.47781.4123-0.42021.49630.1131-0.021-0.54950.16710.01140.04350.19090.2613-0.10960.2305-0.00250.02030.27250.07660.125346.236933.587181.9957
400.95350.2043-0.10520.9631-0.22541.3983-0.1797-0.02420.49930.0585-0.020.1141-0.7384-0.14860.05260.37410.0363-0.11040.0864-0.02130.260231.004364.596735.6087
411.93880.16741.0610.74980.38582.1741-0.0271-0.13240.07160.068-0.06960.0306-0.0841-0.30140.06970.10240.03420.00710.1482-0.01530.084123.564245.094136.8414
423.71612.308-0.87673.8281.85352.5986-0.34820.02670.72040.0196-0.01120.2735-0.4826-0.63010.20790.1810.0767-0.01360.1922-0.06210.150417.907852.056137.5337
431.32250.67950.23422.97360.22611.5526-0.0173-0.3570.36630.204-0.06750.3728-0.3866-0.6975-0.00680.19040.09840.01060.4077-0.07050.205914.708451.631644.1065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 36 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 52 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 89 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 101 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 116 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 136 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 137 through 160 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 175 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 176 through 191 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 192 through 210 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 211 through 225 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 5 through 63 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 64 through 89 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 175 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 176 through 209 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 210 through 222 )B0
17X-RAY DIFFRACTION17chain 'C' and (resid 5 through 89 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 90 through 210 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 211 through 230 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 5 through 89 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 90 through 101 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 102 through 175 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 176 through 223 )D0
24X-RAY DIFFRACTION24chain 'E' and (resid 5 through 89 )E0
25X-RAY DIFFRACTION25chain 'E' and (resid 90 through 101 )E0
26X-RAY DIFFRACTION26chain 'E' and (resid 102 through 136 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 137 through 230 )E0
28X-RAY DIFFRACTION28chain 'F' and (resid 5 through 89 )F0
29X-RAY DIFFRACTION29chain 'F' and (resid 90 through 101 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 102 through 191 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 192 through 230 )F0
32X-RAY DIFFRACTION32chain 'G' and (resid 5 through 63 )G0
33X-RAY DIFFRACTION33chain 'G' and (resid 64 through 89 )G0
34X-RAY DIFFRACTION34chain 'G' and (resid 90 through 101 )G0
35X-RAY DIFFRACTION35chain 'G' and (resid 102 through 116 )G0
36X-RAY DIFFRACTION36chain 'G' and (resid 117 through 136 )G0
37X-RAY DIFFRACTION37chain 'G' and (resid 137 through 175 )G0
38X-RAY DIFFRACTION38chain 'G' and (resid 176 through 210 )G0
39X-RAY DIFFRACTION39chain 'G' and (resid 211 through 230 )G0
40X-RAY DIFFRACTION40chain 'H' and (resid 5 through 89 )H0
41X-RAY DIFFRACTION41chain 'H' and (resid 90 through 175 )H0
42X-RAY DIFFRACTION42chain 'H' and (resid 176 through 191 )H0
43X-RAY DIFFRACTION43chain 'H' and (resid 192 through 222 )H0

+
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://pdbjlvh1.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