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- PDB-4mtk: Crystal structure of PA0091 VgrG1, the central spike of the Type ... -

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Basic information

Entry
Database: PDB / ID: 4mtk
TitleCrystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System
ComponentsVgrG1
KeywordsTOXIN / Beta-barrel / OB-fold / Beta-helix / Type VI secretion system central spike / Secreted outside of the cell
Function / homology
Function and homology information


type VI protein secretion system complex / protein secretion by the type VI secretion system / extracellular region
Similarity search - Function
Light-harvesting Protein - #110 / Pnp Oxidase; Chain A - #50 / Gp5 N-terminal domain / Baseplate protein-like domains / Light-harvesting Protein / Type VI secretion system, RhsGE-associated Vgr family subset / Phage tail baseplate hub (GPD) / Phage tail protein beta-alpha-beta fold / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain ...Light-harvesting Protein - #110 / Pnp Oxidase; Chain A - #50 / Gp5 N-terminal domain / Baseplate protein-like domains / Light-harvesting Protein / Type VI secretion system, RhsGE-associated Vgr family subset / Phage tail baseplate hub (GPD) / Phage tail protein beta-alpha-beta fold / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / 3-Layer(bab) Sandwich / Pnp Oxidase; Chain A / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Type VI secretion system spike protein VgrG1a
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.322 Å
AuthorsSycheva, L.V. / Shneider, M.M. / Leiman, P.G.
CitationJournal: To be Published
Title: The conserved architecture of the T6SS central spike complex
Authors: Sycheva, L.V. / Shneider, M.M. / Basler, M. / Ho, B.T. / Mekalanos, J.J. / Leiman, P.G.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VgrG1
B: VgrG1
C: VgrG1
D: VgrG1
E: VgrG1
F: VgrG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,509264
Polymers432,5906
Non-polymers24,919258
Water1086
1
A: VgrG1
B: VgrG1
C: VgrG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,195147
Polymers216,2953
Non-polymers13,900144
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49630 Å2
ΔGint-185 kcal/mol
Surface area68060 Å2
MethodPISA
2
D: VgrG1
E: VgrG1
F: VgrG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,313117
Polymers216,2953
Non-polymers11,018114
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49530 Å2
ΔGint-191 kcal/mol
Surface area68180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.275, 168.275, 652.849
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 5 - 640 / Label seq-ID: 5 - 640

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF

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Components

#1: Protein
VgrG1


Mass: 72098.375 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA0091, vgrG1 / Plasmid: pTSL2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9I741
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 256 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 6.17 Å3/Da / Density % sol: 80.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4 M Li2SO4, 5% MPD, 100 mM BisTris, 10 mM CsCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2012
RadiationMonochromator: Fixed-exit LN2 cooled double crystal monochromator with Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.32→50 Å / Num. all: 304602 / Num. obs: 304594 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 70.42 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 13.3
Reflection shellResolution: 3.32→3.5 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
RESOLVEmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2P5Z
Resolution: 3.322→49.143 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 18.43 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 6084 2 %Random
Rwork0.1697 ---
all0.1825 304594 --
obs0.1754 304249 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.322→49.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29862 0 1302 6 31170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331614
X-RAY DIFFRACTIONf_angle_d1.00342990
X-RAY DIFFRACTIONf_dihedral_angle_d14.74811424
X-RAY DIFFRACTIONf_chiral_restr0.044284
X-RAY DIFFRACTIONf_plane_restr0.0045592
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18191X-RAY DIFFRACTION12.538TORSIONAL
12B18191X-RAY DIFFRACTION12.538TORSIONAL
13C18191X-RAY DIFFRACTION12.538TORSIONAL
14D18191X-RAY DIFFRACTION12.538TORSIONAL
15E18191X-RAY DIFFRACTION12.538TORSIONAL
16F18191X-RAY DIFFRACTION12.538TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3222-3.360.30491920.30389611X-RAY DIFFRACTION96
3.36-3.39950.3051800.27710002X-RAY DIFFRACTION100
3.3995-3.44090.26391950.25019967X-RAY DIFFRACTION100
3.4409-3.48450.27112360.24069888X-RAY DIFFRACTION100
3.4845-3.53030.26072200.2339961X-RAY DIFFRACTION100
3.5303-3.57870.22541720.229410017X-RAY DIFFRACTION100
3.5787-3.62980.20592100.21149858X-RAY DIFFRACTION100
3.6298-3.68390.22452260.20759962X-RAY DIFFRACTION100
3.6839-3.74150.23931900.201910106X-RAY DIFFRACTION100
3.7415-3.80280.21541680.20169883X-RAY DIFFRACTION100
3.8028-3.86840.21461950.18769915X-RAY DIFFRACTION100
3.8684-3.93870.20782370.16959966X-RAY DIFFRACTION100
3.9387-4.01440.19532190.16819942X-RAY DIFFRACTION100
4.0144-4.09630.16482270.16839945X-RAY DIFFRACTION100
4.0963-4.18530.16692060.14969910X-RAY DIFFRACTION100
4.1853-4.28260.19032250.1539966X-RAY DIFFRACTION100
4.2826-4.38970.17451700.14459919X-RAY DIFFRACTION100
4.3897-4.50830.1832420.1319919X-RAY DIFFRACTION100
4.5083-4.64080.12982340.11979939X-RAY DIFFRACTION100
4.6408-4.79050.14881520.119610029X-RAY DIFFRACTION100
4.7905-4.96160.18951770.13969952X-RAY DIFFRACTION100
4.9616-5.160.16392120.14319902X-RAY DIFFRACTION100
5.16-5.39460.18171960.151910003X-RAY DIFFRACTION100
5.3946-5.67860.17972070.16119938X-RAY DIFFRACTION100
5.6786-6.03380.21521870.17449968X-RAY DIFFRACTION100
6.0338-6.49870.1972030.16939989X-RAY DIFFRACTION100
6.4987-7.15090.21421890.18049897X-RAY DIFFRACTION100
7.1509-8.18160.1811750.17589997X-RAY DIFFRACTION100
8.1816-10.29230.15562270.16339951X-RAY DIFFRACTION100
10.2923-49.14830.24032150.20629863X-RAY DIFFRACTION99
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)
10.0547-0.00480.04920.0539-0.02340.0637-0.04-0.10390.10270.02310.05580.01210.0550.26340.00470.95240.47710.04780.85510.11460.605113.6122-13.115943.1835
20.21760.0742-0.0290.08290.02350.07970.0196-0.07580.0107-0.199-0.01180.05320.1880.19140.01360.94160.39240.04490.56390.04820.592.4366-4.669223.6666
30.1511-0.1172-0.03030.17620.05510.17320.0776-0.04670.0199-0.0871-0.00820.1194-0.1729-0.06990.17480.80120.459-0.02570.24820.00630.5584-43.086854.990927.6464
40.00960.00370.04240.06020.0540.2757-0.05610.0154-0.0187-0.0734-0.07640.00750.1159-0.0455-0.00761.43750.3331-0.07750.49420.00140.8042-8.7781-37.178411.9133
50.00370.01070.00360.0530.00870.02520.03360.0389-0.0718-0.1962-0.08550.03380.2347-0.0574-0.00071.17350.21-0.11490.4706-0.01280.7934-22.0064-19.128713.8516
60.00550.01630.00520.03320.01480.0095-0.0338-0.0035-0.0236-0.0369-0.09530.09090.0024-0.0576-01.41240.1227-0.08910.44270.06280.9692-26.2385-43.657522.3645
70.0085-0.00180.00820.00290.00330.0123-0.1274-0.0418-0.09850.0131-0.0550.08260.0229-0.0718-0.00021.07650.061-0.09790.6220.01350.9555-38.9216-14.099233.0675
8-0.0024-0.0173-0.01780.07540.08910.1131-0.0138-0.0535-0.09720.0839-0.09630.02120.2424-0.10490.00811.09160.1117-0.11260.38590.06450.8052-26.7211-26.03423.6395
90.0005-0.0197-0.01130.2109-0.00830.25510.04030.0782-0.004-0.2359-0.0148-0.00820.0057-0.1717-0.00940.79990.3297-0.10440.34560.04450.5375-36.432240.700619.0918
100.0147-0.0261-0.02230.04720.01920.0707-0.0137-0.02470.02440.0159-0.0476-0.02-0.1610.08970.00261.15890.2935-0.01160.52510.18440.9727-46.244882.937713.2984
110.0011-0.0027-0.00230.00550.00660.01240.1087-0.03690.0157-0.00180.02990.0223-0.0009-0.05210.00011.16820.1451-0.00220.57510.14340.7898-21.7856-35.977854.8553
120.00330.00060.00480.00960.0020.00780.0199-0.0864-0.08160.01230.0412-0.01280.0273-0.038201.24110.0981-0.07420.63850.1780.9252-26.38-38.575453.0473
130.0201-0.00760.00040.01060.00130.0307-0.0178-0.1491-0.0490.02560.05050.130.1397-0.02640.00010.9370.1483-0.02260.61310.12370.6847-27.1618-9.349753.919
140.00670.00210.0119-0.0010.00380.01320.0003-0.1114-0.0789-0.0152-0.0363-0.04320.12370.013800.88870.27010.03290.70210.25730.7076-8.2956-27.701665.9347
150.11150.08-0.06320.0821-0.05130.0664-0.0109-0.1139-0.0805-0.0291-0.06620.03310.220.0822-00.84560.3137-0.00660.66350.08030.5829-11.4874-7.275654.36
160.17360.0121-0.010.02370.04660.13840.0908-0.2112-0.0356-0.0255-0.07490.0982-0.071-0.2555-0.15120.6980.3901-0.10390.42270.00280.5608-42.880339.068126.2158
170.0136-0.015-0.01120.02070.0160.0110.10140.0949-0.0595-0.06850.00280.006-0.1401-0.10730.0531.05140.4993-0.21450.76780.06691.0438-62.741375.093911.5371
180.0125-0.016-0.01030.04920.01660.0831-0.05840.10410.0936-0.1417-0.1019-0.0427-0.40310.2168-00.93510.20240.05750.86390.1490.8363-0.676531.359467.8164
19-0.0013-0.0060.00290.0355-0.0190.0092-0.04650.03930.0912-0.1004-0.0764-0.02-0.04530.03301.20290.13940.05710.85650.07560.9127-0.459250.703777.2763
200.035-0.04890.03130.0341-0.0240.1759-0.06090.00980.0702-0.0255-0.1235-0.1175-0.41450.367-0.00120.94820.01240.12360.93750.12190.841315.537833.994782.1983
210.10590.1313-0.0250.17160.01710.2097-0.04440.0855-0.3096-0.14790.0201-0.35860.18940.59120.17370.58120.67430.33341.56240.19431.112555.0568-22.053472.233
220.0038-0.00210.00550.001-0.00220.00780.02860.0159-0.03410.0243-0.0122-0.0278-0.04490.072400.91940.07890.03970.7442-0.10850.6065-0.352941.5046109.7887
230.0310.011-0.00950.02460.01140.05650.036-0.1810.0813-0.0065-0.1042-0.0058-0.40890.246900.7928-0.0070.02780.9942-0.02440.703911.916930.4928108.3012
240.0037-0.0012-0.00770.0009-0.00430.01580.0669-0.04670.05450.0699-0.07560.1074-0.15020.026700.63340.10060.00960.9873-0.17420.6892-7.839727.3622120.6195
250.01510.0020.01670.0040.01460.0328-0.0085-0.0164-0.01910.0044-0.10760.03330.08490.0656-0.00010.52760.1393-0.01521.12140.06230.63487.16940.2198107.0043
260.06310.01610.09570.0790.0080.1496-0.0589-0.09690.130.1232-0.12720.0548-0.30490.1753-00.69170.12090.03971.21870.00640.70183.744919.1793110.1356
270.11440.08060.01490.05380.00310.09130.0780.0249-0.2213-0.0828-0.203-0.16830.17120.4716-0.25310.4050.33350.18471.48510.24360.917547.7317-5.781983.0661
280.01260.0134-0.00950.0232-0.0093-0.00320.08420.0941-0.0697-0.09280.0549-0.1312-0.00950.1050.14160.73730.76610.28431.61860.03171.650688.6084-37.616767.0964
290.0223-0.0036-0.00490.04140.00240.0137-0.0619-0.0560.0066-0.1110.0384-0.0258-0.0244-0.047500.59290.2118-0.00821.19810.04710.6613-25.84517.773299.757
300.0446-0.01860.05050.0313-0.00210.0620.0926-0.0052-0.1208-0.1038-0.0639-0.03130.0548-0.05650.00010.51770.19270.00461.00130.06390.649-8.2061-1.717589.6952
310.0257-0.00850.00320.0002-0.00210.0080.0012-0.0353-0.1291-0.11940.00650.0501-0.1109-0.04960.00010.59120.2557-0.08330.91210.04850.6899-29.15819.928678.9525
320.0620.0716-0.03810.14680.010.1540.12620.01920.0306-0.2005-0.1178-0.0304-0.02220.012600.61410.25770.00910.98750.05570.6292-6.28825.685874.7505
330.19670.04260.04720.1943-0.05530.16610.09450.0429-0.2131-0.1137-0.0253-0.38130.37110.34740.14750.53830.70660.1571.54170.24091.16355.9365-23.759782.2302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 429 )
3X-RAY DIFFRACTION3chain 'A' and (resid 430 through 640 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 79 )
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 170 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 217 )
7X-RAY DIFFRACTION7chain 'B' and (resid 218 through 282 )
8X-RAY DIFFRACTION8chain 'B' and (resid 283 through 388 )
9X-RAY DIFFRACTION9chain 'B' and (resid 389 through 598 )
10X-RAY DIFFRACTION10chain 'B' and (resid 599 through 640 )
11X-RAY DIFFRACTION11chain 'C' and (resid 5 through 41 )
12X-RAY DIFFRACTION12chain 'C' and (resid 42 through 94 )
13X-RAY DIFFRACTION13chain 'C' and (resid 95 through 170 )
14X-RAY DIFFRACTION14chain 'C' and (resid 171 through 217 )
15X-RAY DIFFRACTION15chain 'C' and (resid 218 through 388 )
16X-RAY DIFFRACTION16chain 'C' and (resid 389 through 598 )
17X-RAY DIFFRACTION17chain 'C' and (resid 599 through 640 )
18X-RAY DIFFRACTION18chain 'D' and (resid 5 through 170 )
19X-RAY DIFFRACTION19chain 'D' and (resid 171 through 217 )
20X-RAY DIFFRACTION20chain 'D' and (resid 218 through 388 )
21X-RAY DIFFRACTION21chain 'D' and (resid 389 through 640 )
22X-RAY DIFFRACTION22chain 'E' and (resid 5 through 41 )
23X-RAY DIFFRACTION23chain 'E' and (resid 42 through 170 )
24X-RAY DIFFRACTION24chain 'E' and (resid 171 through 217 )
25X-RAY DIFFRACTION25chain 'E' and (resid 218 through 282 )
26X-RAY DIFFRACTION26chain 'E' and (resid 283 through 388 )
27X-RAY DIFFRACTION27chain 'E' and (resid 389 through 554 )
28X-RAY DIFFRACTION28chain 'E' and (resid 555 through 640 )
29X-RAY DIFFRACTION29chain 'F' and (resid 5 through 79 )
30X-RAY DIFFRACTION30chain 'F' and (resid 80 through 170 )
31X-RAY DIFFRACTION31chain 'F' and (resid 171 through 217 )
32X-RAY DIFFRACTION32chain 'F' and (resid 218 through 388 )
33X-RAY DIFFRACTION33chain 'F' and (resid 389 through 640 )

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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

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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

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