[English] 日本語
Yorodumi
- PDB-5i7v: Crystal structure of B. pseudomallei FabI in complex with NAD and PT02 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i7v
TitleCrystal structure of B. pseudomallei FabI in complex with NAD and PT02
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / enoyl-ACP reductase / Burkholderia pseudomallei / diphenyl ethers / slow-binding inhibitors
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-phenoxy-5-propyl-phenol / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHirschbeck, M.W. / Eltschkner, S. / Tonge, P.J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 630 Germany
CitationJournal: Biochemistry / Year: 2017
Title: Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase.
Authors: Neckles, C. / Eltschkner, S. / Cummings, J.E. / Hirschbeck, M. / Daryaee, F. / Bommineni, G.R. / Zhang, Z. / Spagnuolo, L. / Yu, W. / Davoodi, S. / Slayden, R.A. / Kisker, C. / Tonge, P.J.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6519
Polymers87,9763
Non-polymers2,6756
Water2,126118
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,86812
Polymers117,3024
Non-polymers3,5678
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area18810 Å2
ΔGint-134 kcal/mol
Surface area31620 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,86812
Polymers117,3024
Non-polymers3,5678
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_365-x-2,-y+1,z1
crystal symmetry operation3_355-x-2,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area18860 Å2
ΔGint-138 kcal/mol
Surface area31570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.620, 111.950, 262.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:258 )
211chain B and (resseq 2:258 )
311chain C and (resseq 2:258 )

-
Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 29325.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria)
Gene: fabI, fabI_2, ACT79_25590, AM256_11615, AM257_11635, AMS56_08605, DP46_2957, DP49_6839, ERS012314_03793, ERS012372_03823, SY87_14645, TR70_1075, VU09_13745
Production host: Escherichia coli (E. coli)
References: UniProt: A0A069B9A4, UniProt: A0A0H3HP34*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PV4 / 2-phenoxy-5-propyl-phenol


Mass: 228.286 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H16O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8 % PEG 1000, 8 % PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.6→43.98 Å / Num. obs: 32230 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.216 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.167 / Mean I/σ(I) obs: 2.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.6.2_432refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EK2
Resolution: 2.6→19.739 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.43
RfactorNum. reflection% reflection
Rfree0.2798 1625 5.07 %
Rwork0.2212 --
obs0.2242 32039 99.96 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 43.2 Å2 / ksol: 0.307 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1487 Å20 Å20 Å2
2--1.0572 Å2-0 Å2
3---2.0915 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5736 0 183 118 6037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086045
X-RAY DIFFRACTIONf_angle_d1.1358202
X-RAY DIFFRACTIONf_dihedral_angle_d23.5922310
X-RAY DIFFRACTIONf_chiral_restr0.072939
X-RAY DIFFRACTIONf_plane_restr0.0041038
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1906X-RAY DIFFRACTIONPOSITIONAL
12B1906X-RAY DIFFRACTIONPOSITIONAL0.052
13C1912X-RAY DIFFRACTIONPOSITIONAL0.056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69270.41971570.33693017X-RAY DIFFRACTION100
2.6927-2.80020.40691750.31252983X-RAY DIFFRACTION100
2.8002-2.92730.30781510.27582999X-RAY DIFFRACTION100
2.9273-3.0810.3131740.26792992X-RAY DIFFRACTION100
3.081-3.27330.35541650.25893014X-RAY DIFFRACTION100
3.2733-3.52470.31681570.25433021X-RAY DIFFRACTION100
3.5247-3.8770.2971570.23393060X-RAY DIFFRACTION100
3.877-4.43240.21881610.17933040X-RAY DIFFRACTION100
4.4324-5.56360.21291590.1723079X-RAY DIFFRACTION100
5.5636-19.73940.22451690.16553209X-RAY DIFFRACTION100
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)
10.9188-0.55170.15691.56420.82420.72230.1772-0.1693-0.54290.2462-0.23560.95740.1133-0.09750.10590.5244-0.103-0.18630.057-0.01760.4788-37.063227.256839.3665
21.2243-0.2796-1.16021.77680.97122.63280.25710.0693-0.02910.2755-0.2896-0.2114-0.1152-0.40530.02520.2350.0089-0.05690.1149-0.06630.0736-22.760433.341835.5902
30.8549-0.6937-0.99243.07111.84671.58970.2620.2459-0.0801-0.2627-0.1293-0.1443-0.5267-0.1228-0.03740.21770.0369-0.07420.1073-0.04530.1189-30.991927.195635.9593
40.09-0.0183-0.11350.49720.12310.75310.27020.1651-0.03350.17040.2551-0.152-0.24540.1208-0.33981.02580.52630.27330.6031-0.16220.4233-23.573130.403121.378
50.4583-0.5954-0.87694.68733.42363.03330.14310.2159-0.2929-0.701-0.2643-0.2124-0.3414-0.2365-0.03840.25750.1493-0.0910.1548-0.12830.2336-28.922525.786528.3355
60.9854-0.502-0.58350.27750.25771.14890.84390.55990.4295-0.9748-0.1535-0.00110.2208-0.21880.69630.29670.3213-0.0427-0.2375-0.6609-1.1318-33.485540.720227.8708
70.6214-0.0178-0.30442.03980.29680.17110.49280.52650.0281-0.9537-0.349-0.1489-0.0913-0.17340.22420.58410.28320.01360.27360.08710.0935-30.351654.195527.4203
80.6648-1.3288-0.57923.72940.45051.0881-0.01210.1342-0.3319-0.0157-0.49311.50520.0802-0.12510.38910.1820.0239-0.0510.1681-0.23350.4726-41.11738.606435.6177
92.72931.5349-2.23038.2218-1.84623.74680.48220.41760.2021.9029-0.3731-0.9933-1.041-0.4392-0.22010.72890.163-0.12850.1068-0.04510.2326-23.744855.199541.1768
102.2181-0.3998-0.28633.81462.62222.1653-0.3589-0.3617-0.09930.9147-0.18530.15280.4722-0.05640.0920.30570.08610.04430.10570.07150.0545-34.265851.270138.4503
111.06640.55960.19493.6890.83580.3525-0.1901-0.17940.29910.9796-0.09910.3880.1209-0.00480.18470.38660.00710.02260.098-0.05510.1674-32.270343.630239.6531
120.5944-0.95240.15984.34690.90950.5256-0.2736-0.1140.65332.53270.0341-2.57060.3119-0.06340.14541.2418-0.0291-1.19820.04690.06441.2298-14.423746.483950.1392
132.63392.80520.34675.72270.31080.13220.89230.04-0.51852.3951-0.4679-0.33360.2043-0.0104-0.4680.8342-0.0408-0.13920.0678-0.06060.1725-32.127434.643947.3638
140.7330.06330.57691.37231.26251.74470.356-0.1111-0.14851.254-0.0866-0.64121.0744-0.0237-0.30960.82-0.1052-0.37590.020.04940.2309-30.782944.082149.2976
150.9349-0.60580.07020.3957-0.05070.0848-0.29980.03190.52650.34420.1829-0.40760.06180.05010.10751.55010.0414-1.03230.064-0.03730.6908-20.230352.756854.8049
160.54451.1479-0.01513.32970.22250.08320.43510.1740.03774.3528-0.06960.1262-0.70320.1019-0.37773.80960.21170.30710.03540.10990.1231-36.927329.423966.6765
170.43050.14450.38121.9268-0.05820.4929-0.11660.0488-0.32282.15970.23880.39430.5903-0.10110.17973.918-0.00280.78430.18030.20640.4351-38.914428.463467.2558
180.55930.8735-0.59682.1708-2.413.3341-0.5751-0.113-0.3418-1.46590.21-0.3350.09180.13350.35212.578-0.13990.37250.7260.4910.8802-44.952629.04181.8586
190.74150.5550.44470.51630.55741.16470.3366-0.3726-0.61032.32310.3051-0.1763-1.3313-0.2631-0.42915.06640.13920.09620.1780.26330.5059-34.983332.25878.5386
201.42390.7820.16230.7647-0.01860.25211.6411-0.3220.05481.5431-0.79650.2145-0.5905-0.0704-0.82235.41010.0668-0.14310.08920.10140.3825-34.63537.270974.1646
211.79210.8438-4.03921.9978-2.4299.65770.4541-0.2232-0.01312.7833-0.00920.7864-1.23460.8218-0.41564.5680.09991.2260.42020.0060.4566-46.968160.618875.5237
222.08410.1323-1.08380.3561-0.92713.13742.1412-0.12760.52420.6856-0.5894-0.0816-0.3372-0.0064-1.49526.59230.0870.32260.0475-0.00750.365-35.419549.805575.1496
230.13690.3938-0.18332.0395-0.32820.35570.26010.0839-0.11422.5346-0.0167-0.23140.2278-0.05950.37133.5583-0.0708-0.3843-0.27340.4211-0.0879-29.164139.895367.072
240.13310.1974-0.10280.7361-0.26240.13280.1835-0.021-0.1261.8405-0.14690.2645-0.45520.0508-0.1684.2777-0.02711.07060.1065-0.00490.2348-42.341253.59764.8052
250.36480.5256-0.26081.7951-0.08351.13431.0554-0.0413-0.44391.3176-0.1002-0.489-0.27640.1116-0.34953.9141-0.2017-1.16140.04240.00930.1824-24.319547.419263.9223
260.46151.0442-0.65314.2558-0.29311.69290.86980.2713-0.00133.2992-0.0775-0.1205-0.2915-0.3665-0.3553.18850.0804-0.22550.008-0.00680.1174-32.380340.955961.0095
271.1198-2.09760.22294.1362-0.93431.4214-0.3056-0.2568-0.5706-1.56030.0713-0.10451.77640.04430.4852.6372-0.05271.11420.4220.06141.2806-54.132444.968367.6964
280.26920.0119-0.30620.8589-0.04640.5834-0.41970.1149-0.40351.0447-0.04511.02550.915-0.14140.53171.3960.03821.22360.01980.1121.2622-52.587142.308653.8418
290.80520.6277-0.0746.2941-0.9330.39010.41930.1424-0.23193.4066-0.24760.0721-0.59330.11960.02241.9466-0.2384-0.1060.08230.00510.0245-32.835937.257255.9992
300.10760.0215-0.05450.76840.05640.26260.0991-0.10380.17510.8163-0.30560.49930.4843-0.18430.27361.2184-0.1390.77480.0467-0.07070.6656-48.676150.24249.7311
311.82990.04470.34891.180.10480.08660.37030.0495-0.32240.3507-0.33820.88350.41220.1198-0.11460.18310.1017-0.05280.03780.00950.7264-68.367241.298926.9332
320.4596-0.4098-0.00940.6717-0.01510.04990.1321-0.0987-0.41680.1624-0.0912-0.1539-0.0411-0.04110.04970.24390.0384-0.21990.05340.18151.2701-60.328842.837124.7217
331.164-0.94030.02161.2452-0.1230.22020.2676-0.022-0.1947-0.2124-0.33220.40040.0930.31850.1504-0.32850.0567-0.320.05840.20230.9158-62.91833.390928.5989
341.0963-0.3843-0.51050.21260.18310.6947-0.34990.0228-0.69430.13930.04770.67080.2679-0.09590.3330.18860.09740.15260.08150.07250.8856-73.252730.745523.0918
350.047-0.13620.07811.0599-0.30660.34730.1191-0.0482-0.09060.21820.17630.072-0.061-0.0023-0.26330.28450.19480.05680.08610.09761.2282-56.188331.34474.673
361.446-0.05470.56490.85070.18611.28030.61790.00920.2335-0.2651-0.0924-0.26890.1198-0.1506-0.32670.09290.05930.11790.00420.05410.8571-60.889732.1185-1.2367
370.6593-0.4172-0.08086.27981.7690.9880.1840.06710.73610.84940.22260.16780.23140.0354-0.46720.1466-0.0349-0.10230.06380.06191.0993-73.865234.799811.1653
381.9382-0.0486-1.0220.03240.03440.801-0.0124-0.58720.7627-0.03930.49090.31340.05180.3992-0.2023-0.289-0.0165-0.37230.19620.06051.0042-75.655541.08217.1584
391.9751-0.09360.90310.6125-0.05650.4091-0.08340.00010.08030.25220.3513-0.0963-0.1108-0.0346-0.33310.09470.0625-0.10120.0996-0.05840.9478-61.725243.26732.1061
400.157-0.0656-0.25920.97470.00910.5822-0.0088-0.1789-0.36730.4197-0.05640.2074-0.1296-0.09960.1396-0.23130.1432-0.09510.01420.04610.9054-72.448844.860312.5693
410.6223-0.57730.32510.8581-0.32540.20750.33570.0350.93820.05170.11060.59-0.09490.1307-0.51490.11430.16720.21630.3904-0.06272.0605-49.543240.38028.1399
420.14920.0782-0.04270.0830.02330.4130.17420.0871-0.21420.14910.39460.10270.1417-0.0163-0.31770.11940.22-0.17870.2553-0.13681.0001-51.146654.060212.7717
430.3269-0.0419-0.39340.01630.05460.4488-0.01520.4218-0.1877-0.3347-0.13380.00650.1718-0.24450.1164-0.00720.1418-0.0819-00.02840.6925-71.583351.654621.2996
444.26250.77824.28870.17610.76524.32220.3117-0.3262-0.09720.18010.0811-0.21950.1591-0.5917-0.37570.13140.0547-0.28320.28540.01010.8563-66.031453.128411.9629
450.13470.0099-0.07480.2493-0.2350.2415-0.0007-0.03460.1539-0.11920.11290.28770.0974-0.0464-0.1776-0.027-0.0526-0.13270.22050.06680.5147-55.22758.6264.604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:12)
2X-RAY DIFFRACTION2(chain A and resid 13:25)
3X-RAY DIFFRACTION3(chain A and resid 26:40)
4X-RAY DIFFRACTION4(chain A and resid 41:49)
5X-RAY DIFFRACTION5(chain A and resid 50:63)
6X-RAY DIFFRACTION6(chain A and resid 64:105)
7X-RAY DIFFRACTION7(chain A and resid 106:124)
8X-RAY DIFFRACTION8(chain A and resid 125:146)
9X-RAY DIFFRACTION9(chain A and resid 147:158)
10X-RAY DIFFRACTION10(chain A and resid 159:171)
11X-RAY DIFFRACTION11(chain A and resid 172:202)
12X-RAY DIFFRACTION12(chain A and resid 203:218)
13X-RAY DIFFRACTION13(chain A and resid 219:241)
14X-RAY DIFFRACTION14(chain A and resid 242:249)
15X-RAY DIFFRACTION15(chain A and resid 250:258)
16X-RAY DIFFRACTION16(chain B and resid 2:18)
17X-RAY DIFFRACTION17(chain B and resid 19:40)
18X-RAY DIFFRACTION18(chain B and resid 41:50)
19X-RAY DIFFRACTION19(chain B and resid 51:75)
20X-RAY DIFFRACTION20(chain B and resid 76:100)
21X-RAY DIFFRACTION21(chain B and resid 101:112)
22X-RAY DIFFRACTION22(chain B and resid 113:126)
23X-RAY DIFFRACTION23(chain B and resid 127:149)
24X-RAY DIFFRACTION24(chain B and resid 150:168)
25X-RAY DIFFRACTION25(chain B and resid 169:178)
26X-RAY DIFFRACTION26(chain B and resid 179:192)
27X-RAY DIFFRACTION27(chain B and resid 193:204)
28X-RAY DIFFRACTION28(chain B and resid 205:224)
29X-RAY DIFFRACTION29(chain B and resid 225:247)
30X-RAY DIFFRACTION30(chain B and resid 248:258)
31X-RAY DIFFRACTION31(chain C and resid 2:17)
32X-RAY DIFFRACTION32(chain C and resid 18:28)
33X-RAY DIFFRACTION33(chain C and resid 29:55)
34X-RAY DIFFRACTION34(chain C and resid 56:92)
35X-RAY DIFFRACTION35(chain C and resid 93:99)
36X-RAY DIFFRACTION36(chain C and resid 100:120)
37X-RAY DIFFRACTION37(chain C and resid 121:128)
38X-RAY DIFFRACTION38(chain C and resid 129:147)
39X-RAY DIFFRACTION39(chain C and resid 148:167)
40X-RAY DIFFRACTION40(chain C and resid 168:195)
41X-RAY DIFFRACTION41(chain C and resid 196:204)
42X-RAY DIFFRACTION42(chain C and resid 205:223)
43X-RAY DIFFRACTION43(chain C and resid 224:242)
44X-RAY DIFFRACTION44(chain C and resid 243:248)
45X-RAY DIFFRACTION45(chain C and resid 249:258)

+
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