[English] 日本語
Yorodumi
- PDB-4jd9: Contact pathway inhibitor from a sand fly -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jd9
TitleContact pathway inhibitor from a sand fly
Components14.5 kDa salivary protein
KeywordsPROTEIN BINDING / Odorant-binding protein / Binding protein / glycosaminoglycan / polyphosphate
Function / homologyPheromone/general odorant binding protein domain / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha / 14.5 kDa salivary protein
Function and homology information
Biological speciesPhlebotomus duboscqi (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.601 Å
AuthorsAndersen, J.F. / Xu, X. / Alvarenga, P.
CitationJournal: Arterioscler Thromb Vasc Biol / Year: 2013
Title: Novel family of insect salivary inhibitors blocks contact pathway activation by binding to polyphosphate, heparin, and dextran sulfate.
Authors: Alvarenga, P.H. / Xu, X. / Oliveira, F. / Chagas, A.C. / Nascimento, C.R. / Francischetti, I.M. / Juliano, M.A. / Juliano, L. / Scharfstein, J. / Valenzuela, J.G. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionFeb 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14.5 kDa salivary protein
B: 14.5 kDa salivary protein
C: 14.5 kDa salivary protein
D: 14.5 kDa salivary protein
F: 14.5 kDa salivary protein
E: 14.5 kDa salivary protein
G: 14.5 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,86750
Polymers101,7367
Non-polymers4,13143
Water5,152286
1
A: 14.5 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0146
Polymers14,5341
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 14.5 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2068
Polymers14,5341
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 14.5 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0146
Polymers14,5341
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 14.5 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1107
Polymers14,5341
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: 14.5 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2068
Polymers14,5341
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: 14.5 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1107
Polymers14,5341
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: 14.5 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2068
Polymers14,5341
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.956, 97.119, 236.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
14.5 kDa salivary protein / PdSP15b


Mass: 14533.743 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phlebotomus duboscqi (insect) / Gene: K03, M03 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q06K46
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 4.22 Å3/Da / Density % sol: 70.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.6 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 22, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 53287 / Num. obs: 53283 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.161 / Χ2: 1.715 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.644.60.59524240.907193.6
2.64-2.695.10.56726400.904198.1
2.69-2.745.80.52826370.937199.4
2.74-2.86.40.50826200.973199.8
2.8-2.867.20.47926400.996199.6
2.86-2.937.80.46726470.99199.7
2.93-38.50.42526491.085199.7
3-3.0890.38426471.106199.7
3.08-3.179.40.33726461.257199.7
3.17-3.289.70.2926601.359199.8
3.28-3.399.90.24926681.502199.7
3.39-3.539.80.19626601.689199.9
3.53-3.699.70.1626721.928199.9
3.69-3.889.70.14526911.981199.7
3.88-4.139.50.12226762.229199.8
4.13-4.459.40.1126892.436199.7
4.45-4.899.20.09527222.5871100
4.89-5.69.30.09427402.4261100
5.6-7.059.20.08927572.3241100
7.05-5080.05229132.8199.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.14 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å48.56 Å
Translation2.6 Å48.56 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.601→46.369 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8332 / SU ML: 0.87 / σ(F): 1.34 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 2709 5.08 %
Rwork0.1968 --
obs0.1988 53283 98.93 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.044 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 157.82 Å2 / Biso mean: 45.5332 Å2 / Biso min: 9.18 Å2
Baniso -1Baniso -2Baniso -3
1-3.9161 Å2-0 Å20 Å2
2---3.9809 Å20 Å2
3---0.0648 Å2
Refinement stepCycle: LAST / Resolution: 2.601→46.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6941 0 215 286 7442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087265
X-RAY DIFFRACTIONf_angle_d1.1019711
X-RAY DIFFRACTIONf_chiral_restr0.078985
X-RAY DIFFRACTIONf_plane_restr0.0051186
X-RAY DIFFRACTIONf_dihedral_angle_d15.7972768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6011-2.64840.29741300.27722286241687
2.6484-2.69930.34831440.2682614275898
2.6993-2.75440.32051380.26282625276399
2.7544-2.81430.29441510.238926322783100
2.8143-2.87980.31741320.244526792811100
2.8798-2.95180.30291240.236126462770100
2.9518-3.03160.34261280.227626742802100
3.0316-3.12070.24651470.230126582805100
3.1207-3.22150.26671460.229526442790100
3.2215-3.33660.26671370.216226642801100
3.3366-3.47010.25281450.193626772822100
3.4701-3.6280.20651520.168126582810100
3.628-3.81920.16831350.169326872822100
3.8192-4.05830.23271530.157127012854100
4.0583-4.37150.20091600.150626822842100
4.3715-4.8110.19221540.148226772831100
4.811-5.50610.18961490.173527402889100
5.5061-6.93340.26931440.223727822926100
6.9334-46.37660.20141400.20322848298898
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)
16.56850.1101-6.21148.0176-1.73376.30910.34040.0777-0.2453-0.7173-0.1870.8949-0.3794-0.5065-0.41640.64290.0524-0.22810.6935-0.11080.4387-31.75034.8939-5.9084
23.66541.1648-0.2541.90520.55594.74430.00310.6233-0.0123-0.250.18350.1148-0.2124-0.558-0.12050.647-0.0116-0.11170.29040.00680.1532-23.24045.5933-3.3579
30.4319-0.4126-0.14250.90590.87391.11530.253-0.02210.1942-0.3506-0.08-0.0762-0.78660.17450.57460.9413-0.10320.06940.20550.08320.1213-14.723315.5731-5.5675
40.9028-0.01130.03030.71220.84661.30840.0551-0.15620.32430.02210.1665-0.1339-0.73240.3588-0.03010.8455-0.35650.09940.4516-0.09330.191-9.337217.20982.5117
52.2434-0.7338-0.56745.41713.2955.52820.1259-0.33170.11920.07360.3233-0.2866-0.32550.2944-0.44620.5454-0.15430.03850.3031-0.04760.13-13.40357.90564.2505
62.78430.61432.36821.0798-0.31635.1257-0.00660.23920.3114-0.2664-0.18250.0757-0.4911-0.24370.04490.95390.2450.03610.39580.10690.3077-27.797417.97710.2587
78.8126-5.20590.75415.23822.34246.180.3630.01970.8689-0.3813-0.1157-1.0504-1.3177-0.1294-0.18650.5591-0.15950.04380.40840.17650.3986-6.87951.6136-38.7129
81.17850.55020.15046.28490.48864.9656-0.4330.09470.1036-0.38820.40830.1527-0.55510.48470.05310.32460.02910.01390.25310.12890.1519-12.0192-4.7111-37.065
91.24450.87520.02762.0898-0.26712.44510.00050.34490.2606-0.0214-0.14560.1928-0.3853-0.24620.00260.13370.06350.00380.17660.09440.1196-19.4323-10.3184-40.7949
103.9-2.57325.36195.9269-4.39087.5420.63670.422-0.3968-1.0825-0.3746-0.37110.73760.2842-0.01580.29980.11520.04740.2390.04190.1793-13.5608-20.7177-38.3388
110.2450.08380.43281.78922.55664.0580.1234-0.1421-1.1075-0.7575-0.3571-0.55341.11120.54450.27930.27360.03870.01160.1830.03630.4829-6.0889-23.9279-30.9192
127.014-3.76721.71746.2126-2.32233.6035-0.1901-0.9-0.75140.10490.46460.39090.3066-0.0358-0.07660.2339-0.02690.0320.19810.08460.0904-22.9943-19.6525-31.3612
131.5164-0.18352.03062.0738-0.37723.1093-0.1241-0.50970.02880.3910.1267-0.0118-0.1385-0.00820.03440.19830.01850.01620.28740.01810.0225-20.397-10.1231-29.5433
145.47410.31130.95567.0714-5.09864.8532-0.23960.17540.032-0.1022-0.2716-0.42120.02341.05280.49630.1260.09580.01260.2657-0.0350.1857-3.0618-13.2376-33.6454
157.15392.0731-1.40954.1297-1.53623.38990.09460.31290.67510.04560.4690.5336-0.8474-0.3328-0.57611.03-0.0279-0.01260.29990.13370.3214-16.088113.5841-22.6815
167.6573-2.3565-4.8233.80040.248.34860.23540.8587-0.0417-0.5603-0.32850.1927-0.8905-0.0779-0.09210.6369-0.1424-0.09280.40860.00730.1429-14.2235.54-20.2161
172.6514-0.39291.53192.0587-1.9518.02310.3899-0.10960.0558-0.1894-0.0089-0.03930.07680.3022-0.23740.306-0.1210.03380.5008-0.04340.1433-8.8699-2.9571-23.9594
184.14043.08981.28538.13322.1193.61440.07060.17530.266-0.05170.4293-1.0961-0.47231.1744-0.11480.4439-0.36850.14010.7912-0.15650.42893.69972.3259-19.5111
194.26142.71672.02792.99770.95212.88860.4175-0.0595-0.11180.58720.0121-0.35740.09161.0222-0.36380.39690.1277-0.01240.8107-0.1450.1523-0.5837-8.3036-14.6726
206.72371.67114.39553.75252.16973.86180.0811-0.4076-0.12110.54340.2163-0.1622-0.29220.4323-0.14670.3701-0.0560.0240.4111-0.04270.1095-9.4079-3.8957-12.6592
211.3654-0.49840.30932.73610.71536.0396-0.1320.05770.0649-0.0616-0.25740.041-0.83690.08050.09410.7438-0.41330.07730.7375-0.16280.2653-2.512812.2636-16.6243
221.2642-2.05020.17645.8847-3.40873.8337-0.0570.424-0.72720.13310.2168-0.13760.92580.4453-0.23370.77060.0873-0.0670.4023-0.15210.3894-25.5262-11.708111.5485
234.46770.78970.39453.025-1.09684.57940.1180.3631-0.0144-0.41850.16720.0933-0.1181-0.2333-0.19980.34530.0988-0.03790.25630.00120.1098-32.18442.543312.9873
243.76210.5873-1.02161.7554-0.11981.81570.1798-0.51150.58670.11610.15270.3028-0.8238-0.31770.23060.67910.30910.02550.39190.09890.2907-32.015613.965719.2583
253.53480.3709-1.0563.1422-1.3254.71890.12760.2774-0.0331-0.0040.10530.2024-0.4961-0.3986-0.2230.3290.0771-0.02490.27770.07590.1251-31.14731.388719.3998
265.23494.25641.22794.19340.12262.7531-0.01470.2096-0.014-0.32390.3033-1.0677-0.02881.0753-0.22950.27420.02730.19350.5320.030.5439-14.6074-11.63-55.9035
274.62030.3322-0.96581.7497-0.56153.28860.03370.20630.1726-0.182-0.1926-0.35440.14730.67420.20110.2071-0.07780.0790.20410.02860.1853-20.8485-6.9492-53.8499
284.17890.3254-2.21233.65520.26653.6902-0.0102-0.21190.331-0.1510.2608-0.2348-0.4820.2801-0.14330.1405-0.0425-0.01470.0927-0.02480.1575-29.1475-1.6343-57.5988
291.31661.0406-2.20275.2114-4.82527.759-0.16390.3312-0.4275-0.62060.22660.45140.0945-0.4732-0.13060.1362-0.00250.0270.1499-0.06390.2546-37.7599-9.9736-55.392
304.7756-1.70312.35134.1451.86383.2224-0.397-0.0134-0.64480.37250.09960.660.1559-0.392-0.00470.1953-0.02950.10120.1517-0.02490.4175-38.8649-18.0477-47.8897
315.63372.8491-1.79145.0366-2.36893.76460.2486-0.01820.06780.5271-0.27670.4835-0.331-0.21610.04010.06930.03480.02620.1451-0.03880.187-39.0135-0.7163-48.1858
322.29861.3747-0.28296.1355-2.22762.5782-0.0078-0.32040.08480.4356-0.0858-0.1708-0.18040.10690.05110.14820.0674-0.00670.0912-0.02780.0973-29.1341-0.8329-46.3227
336.84210.2923-4.52394.6198-1.15656.3458-0.31260.1711-0.842-0.2316-0.5195-0.26380.08110.48910.43030.1661-0.03410.01990.1508-0.05290.266-27.8264-18.1884-50.5847
343.2011-2.1445-0.27323.8736-0.65741.55030.0589-0.2173-0.44060.58220.4217-1.14060.56920.96-0.3840.35470.151-0.22490.5695-0.0970.4817-47.0809-38.5739-28.4583
352.5094-0.2190.15642.3122-1.37382.8191-0.0988-0.34230.06760.37460.1227-0.19620.12830.0232-0.01710.19610.121-0.15370.1708-0.010.0738-62.6001-34.9822-29.8549
361.212-0.5557-0.02847.1937-2.83993.02130.268-0.03010.0169-0.8063-0.17240.41080.5223-0.46790.00590.10790.03240.00570.3637-0.050.1629-73.2436-38.1811-36.2975
372.06040.2586-0.69654.9884-1.01333.1512-0.0163-0.13570.1318-0.13740.06-0.0880.193-0.2799-0.0510.12860.01620.0230.1876-0.00760.0863-60.9143-36.1487-36.4055
383.00933.8391-0.75226.73630.64021.57920.2352-0.3397-0.99920.0640.1319-0.05750.5477-0.12660.0020.6340.0568-0.00350.17140.18830.4675-43.4243-54.6962-44.6321
396.0226-0.5496-0.83286.8274-2.91375.61420.0567-0.2659-0.5320.2478-0.05240.17941.3303-0.35840.01460.4291-0.0617-0.0210.2570.07520.1206-48.7864-49.0972-47.4921
402.0832-0.2223-1.17262.44690.35423.4925-0.1559-0.10860.0459-0.0240.02220.25480.377-0.36150.03560.174-0.0146-0.06410.21570.06160.1249-51.5909-38.5358-43.6273
415.4568-0.2823-4.32361.803-0.75555.56930.3449-0.9186-0.03020.3193-0.0064-0.5111-0.35880.4858-0.24770.189-0.0316-0.07670.1581-0.03450.241-41.5101-32.1115-46.2858
425.925-3.71972.8984.46681.35496.14550.2230.06210.0923-0.2004-0.1395-0.5267-0.53770.50510.02090.2057-0.13540.01520.169-0.05250.4714-33.527-32.9866-53.8006
435.29140.8354-1.83651.4547-0.5712.076-0.1550.54390.2242-0.25680.22630.0848-0.0872-0.46590.00130.19530.0128-0.04150.0788-0.00060.1473-51.043-29.2968-53.3426
447.40742.7388-5.84484.7760.06346.33060.16230.2884-0.0891-0.1405-0.1106-0.0040.067-0.3949-0.01140.14550.0514-0.05510.11860.00430.113-54.7348-39.9566-53.5425
455.1642-1.37851.45225.2358-0.29162.46920.15190.0105-0.1219-0.0162-0.1134-0.23240.30170.3114-0.1160.12920.00170.00360.075-0.0340.2271-36.8073-41.2158-52.9841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:12 )A1 - 12
2X-RAY DIFFRACTION2( CHAIN A AND RESID 17:29 )A17 - 29
3X-RAY DIFFRACTION3( CHAIN A AND RESID 30:52 )A30 - 52
4X-RAY DIFFRACTION4( CHAIN A AND RESID 53:81 )A53 - 81
5X-RAY DIFFRACTION5( CHAIN A AND RESID 82:105 )A82 - 105
6X-RAY DIFFRACTION6( CHAIN A AND RESID 106:122 )A106 - 122
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:17 )B1 - 17
8X-RAY DIFFRACTION8( CHAIN B AND RESID 18:29 )B18 - 29
9X-RAY DIFFRACTION9( CHAIN B AND RESID 30:39 )B30 - 39
10X-RAY DIFFRACTION10( CHAIN B AND RESID 40:52 )B40 - 52
11X-RAY DIFFRACTION11( CHAIN B AND RESID 53:57 )B53 - 57
12X-RAY DIFFRACTION12( CHAIN B AND RESID 58:81 )B58 - 81
13X-RAY DIFFRACTION13( CHAIN B AND RESID 82:105 )B82 - 105
14X-RAY DIFFRACTION14( CHAIN B AND RESID 106:122 )B106 - 122
15X-RAY DIFFRACTION15( CHAIN C AND RESID 1:12 )C1 - 12
16X-RAY DIFFRACTION16( CHAIN C AND RESID 13:29 )C13 - 29
17X-RAY DIFFRACTION17( CHAIN C AND RESID 30:39 )C30 - 39
18X-RAY DIFFRACTION18( CHAIN C AND RESID 40:57 )C40 - 57
19X-RAY DIFFRACTION19( CHAIN C AND RESID 58:81 )C58 - 81
20X-RAY DIFFRACTION20( CHAIN C AND RESID 82:105 )C82 - 105
21X-RAY DIFFRACTION21( CHAIN C AND RESID 106:122 )C106 - 122
22X-RAY DIFFRACTION22( CHAIN D AND RESID 1:16 )D1 - 16
23X-RAY DIFFRACTION23( CHAIN D AND RESID 17:57 )D17 - 57
24X-RAY DIFFRACTION24( CHAIN D AND RESID 58:81 )D58 - 81
25X-RAY DIFFRACTION25( CHAIN D AND RESID 82:122 )D82 - 122
26X-RAY DIFFRACTION26( CHAIN F AND RESID 1:16 )F1 - 16
27X-RAY DIFFRACTION27( CHAIN F AND RESID 17:29 )F17 - 29
28X-RAY DIFFRACTION28( CHAIN F AND RESID 30:39 )F30 - 39
29X-RAY DIFFRACTION29( CHAIN F AND RESID 40:52 )F40 - 52
30X-RAY DIFFRACTION30( CHAIN F AND RESID 53:57 )F53 - 57
31X-RAY DIFFRACTION31( CHAIN F AND RESID 58:81 )F58 - 81
32X-RAY DIFFRACTION32( CHAIN F AND RESID 82:105 )F82 - 105
33X-RAY DIFFRACTION33( CHAIN F AND RESID 106:122 )F106 - 122
34X-RAY DIFFRACTION34( CHAIN E AND RESID 1:17 )E1 - 17
35X-RAY DIFFRACTION35( CHAIN E AND RESID 18:57 )E18 - 57
36X-RAY DIFFRACTION36( CHAIN E AND RESID 58:81 )E58 - 81
37X-RAY DIFFRACTION37( CHAIN E AND RESID 82:122 )E82 - 122
38X-RAY DIFFRACTION38( CHAIN G AND RESID 1:12 )G1 - 12
39X-RAY DIFFRACTION39( CHAIN G AND RESID 13:29 )G13 - 29
40X-RAY DIFFRACTION40( CHAIN G AND RESID 30:39 )G30 - 39
41X-RAY DIFFRACTION41( CHAIN G AND RESID 40:52 )G40 - 52
42X-RAY DIFFRACTION42( CHAIN G AND RESID 53:57 )G53 - 57
43X-RAY DIFFRACTION43( CHAIN G AND RESID 58:82 )G58 - 82
44X-RAY DIFFRACTION44( CHAIN G AND RESID 83:100 )G83 - 100
45X-RAY DIFFRACTION45( CHAIN G AND RESID 101:122 )G101 - 122

+
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