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- PDB-5akn: THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TAR... -

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Basic information

Entry
Database: PDB / ID: 5akn
TitleTHE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE non-CODING STRAND B AND IN THE PRESENCE OF 2MM MN
Components
  • 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
  • 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP *CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
  • 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
  • 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3
  • 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
  • D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
  • HOMING ENDONUCLEASE I-DMOI
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / HYDROLASE / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES
Function / homology
Function and homology information


intein-mediated protein splicing / intron homing / endonuclease activity / Hydrolases; Acting on ester bonds
Similarity search - Function
LAGLIDADG-like domain / Intein / Homing endonucleases / Endonuclease I-creI / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Homing endonuclease I-DmoI
Similarity search - Component
Biological speciesDESULFUROCOCCUS MOBILIS (archaea)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMolina, R. / Marcaida, M.J. / Redondo, P. / Marenchino, M. / D'Abramo, M. / Montoya, G. / Prieto, J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold.
Authors: Molina, R. / Marcaida, M.J. / Redondo, P. / Marenchino, M. / Duchateau, P. / D'Abramo, M. / Montoya, G. / Prieto, J.
History
DepositionMar 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_detector / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_detector.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: HOMING ENDONUCLEASE I-DMOI
B: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
C: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3
D: D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
E: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
F: HOMING ENDONUCLEASE I-DMOI
G: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
H: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
J: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
K: HOMING ENDONUCLEASE I-DMOI
L: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP *CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
M: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
O: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,46819
Polymers120,13913
Non-polymers3306
Water3,459192
1
A: HOMING ENDONUCLEASE I-DMOI
B: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
C: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3
D: D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
E: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5937
Polymers38,4835
Non-polymers1102
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-51.5 kcal/mol
Surface area14050 Å2
MethodPISA
2
F: HOMING ENDONUCLEASE I-DMOI
G: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
H: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
J: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6386
Polymers38,5284
Non-polymers1102
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-36.4 kcal/mol
Surface area14400 Å2
MethodPISA
3
K: HOMING ENDONUCLEASE I-DMOI
L: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP *CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
M: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
O: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2386
Polymers43,1284
Non-polymers1102
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-34 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.100, 70.340, 107.170
Angle α, β, γ (deg.)90.00, 119.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules AFK

#1: Protein HOMING ENDONUCLEASE I-DMOI


Mass: 23210.021 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFUROCOCCUS MOBILIS (archaea) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS
References: UniProt: P21505, Hydrolases; Acting on ester bonds

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DNA chain , 6 types, 10 molecules BGCDEJOHML

#2: DNA chain 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'


Mass: 4296.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3


Mass: 3366.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'


Mass: 4554.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: DNA chain 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'


Mass: 3055.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#6: DNA chain 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'


Mass: 7966.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#7: DNA chain 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP *CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'


Mass: 8896.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 2 types, 198 molecules

#8: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.37 Å3/Da / Density % sol: 54 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.8929
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8929 Å / Relative weight: 1
ReflectionResolution: 2.75→46.5 Å / Num. obs: 68711 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 51.06 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.3
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.5 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VS7

2vs7


Resolution: 2.75→46.49 Å / SU ML: 0.48 / σ(F): 1.3 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 3415 5 %
Rwork0.175 --
obs0.178 68508 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.21 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.6981 Å20 Å20.873 Å2
2--9.1106 Å20 Å2
3----3.4125 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4486 3075 6 192 7759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078140
X-RAY DIFFRACTIONf_angle_d1.34311645
X-RAY DIFFRACTIONf_dihedral_angle_d24.3723259
X-RAY DIFFRACTIONf_chiral_restr0.0651313
X-RAY DIFFRACTIONf_plane_restr0.004943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.84830.35963400.2776421X-RAY DIFFRACTION96
2.8483-2.96230.27573370.25196426X-RAY DIFFRACTION96
2.9623-3.09710.32933400.22986448X-RAY DIFFRACTION96
3.0971-3.26040.26743420.19676469X-RAY DIFFRACTION97
3.2604-3.46460.25223430.17486570X-RAY DIFFRACTION97
3.4646-3.7320.21743340.15226429X-RAY DIFFRACTION97
3.732-4.10730.19073500.13266596X-RAY DIFFRACTION98
4.1073-4.70120.19123440.12756560X-RAY DIFFRACTION98
4.7012-5.92110.21973410.13536606X-RAY DIFFRACTION99
5.9211-46.50030.19243440.16236568X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.10070.967-2.04342.03330.32253.3755-0.20880.329-0.19350.1660.1895-0.0780.3774-0.5715-0.06870.126-0.0149-0.02460.15020.06190.185811.78431.872129.1776
23.2541.0021-1.83221.0568-0.171.2421-0.45190.3771-0.60620.11160.1195-0.07780.5603-0.42780.6540.2421-0.12390.13230.135-0.00560.16589.167922.714529.131
31.46990.1145-1.3490.5256-0.14252.43540.0252-0.0317-0.16120.1038-0.0349-0.24650.11210.09140.01270.20160.00990.03830.01510.0470.245528.275231.797725.6717
47.2108-0.8976-3.10590.3691-0.08262.1237-0.23931.62380.7503-0.11340.3549-0.30130.3755-0.7309-0.1230.23250.01730.09970.42270.15270.270931.809338.33898.5375
54.50260.3637-2.51450.81750.04163.28420.15071.28391.01390.00450.39250.28270.3805-0.7887-0.44170.2458-0.02310.10160.53310.17840.2539-1.532637.75631.8001
69.10812.4666-7.25480.7385-2.52479.98190.24181.12931.75-0.18430.53560.40270.3922-1.6094-0.65860.13650.05210.10570.35650.15280.30813.175739.178328.0561
75.2845-0.76330.93390.9804-0.58780.5069-0.33091.0716-0.22990.16940.0408-0.51720.57710.11980.24230.29390.06280.06740.6326-0.00720.3538.553338.64976.5872
81.44080.17891.68860.2867-0.12932.49610.0612-0.3664-0.3695-0.03820.0147-0.10890.1238-0.5127-0.15840.18180.05390.0356-0.01220.08170.205636.2021-5.598122.1508
93.415-0.86791.79821.9773-0.57131.16440.02340.70360.069-0.4766-0.1329-0.4463-0.08530.38050.02530.19620.01630.07050.12560.00720.11342.0173-2.5680.9394
100.02530.0926-0.00221.37370.67640.4548-0.0850.04390.0576-0.6569-0.0188-0.2714-0.4779-0.0150.04360.98060.13780.09370.6152-0.06760.689732.8105-14.22336.1834
114.23951.6702-0.49382.60820.08330.2754-0.23611.37470.1053-0.59820.7992-0.1337-0.7649-0.86950.18950.50780.1459-0.11360.49580.234-0.022529.17235.3596-6.3174
121.6867-0.53740.0450.20430.38523.63560.1182-0.5488-0.08590.32540.38490.0414-1.8901-0.7501-0.2320.38140.1105-0.04120.2980.12360.138632.16513.434.2759
135.533-0.48310.80080.6743-0.74422.77580.1838-1.0644-0.03330.26390.33610.2421-1.1046-1.0422-0.18880.40750.13580.01920.0434-0.03240.153931.30545.085628.0961
141.53980.0404-1.67230.28870.00171.88150.43381.810.0184-0.46880.6241-0.1952-0.2387-0.6354-0.99250.6472-0.03810.00451.4085-0.01120.229330.98295.486-13.2144
153.11340.12370.68211.2315-0.09290.34980.03620.4895-0.41870.1163-0.02480.1625-0.14430.0453-0.00510.081-0.02570.03460.1188-0.03640.1278-31.9718-8.453738.8714
161.24811.16120.70591.52370.36920.5625-0.03160.1258-0.13180.08820.03490.21410.181-0.2104-0.01560.1094-0.0157-0.03370.12470.00040.1405-27.2246-6.242444.2961
173.2643-1.28970.22071.0393-0.65851.6445-0.0285-0.61390.03560.3470.2918-0.1419-0.3184-0.081-0.12730.1379-0.0096-0.05070.09170.06290.194-14.9391-2.469953.4015
183.49260.7715-1.34061.75950.69734.1139-0.50550.4498-0.39590.01840.4952-0.5571-0.59670.4471-0.09880.1301-0.0557-0.03470.3178-0.04590.3407-3.39092.1544.5841
192.4362-0.8085-1.37761.6571-0.56331.5943-0.78421.26550.1004-0.24410.31450.2607-0.4674-0.17920.33130.154-0.1538-0.12210.43130.11940.2965-40.16230.456826.8268
209.33471.54972.36861.35640.07591.1721-0.95950.9037-0.4197-0.41780.47930.0332-0.60730.09810.18830.1812-0.0988-0.0420.40170.04380.1804-34.23441.892829.0031
214.8556-1.07184.47941.3675-1.28314.6519-0.44350.3362-0.82690.38780.6535-0.0969-0.53620.619-0.16150.2670.0146-0.0530.3965-0.08190.28531.78042.832649.9038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:48)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 49:75)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 76:183)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:14)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 15:25)
6X-RAY DIFFRACTION6(CHAIN D AND RESID 1:15)
7X-RAY DIFFRACTION7(CHAIN E AND RESID 16:25)
8X-RAY DIFFRACTION8(CHAIN F AND RESID 5:95)
9X-RAY DIFFRACTION9(CHAIN F AND RESID 96:183)
10X-RAY DIFFRACTION10(CHAIN F AND RESID 184:189)
11X-RAY DIFFRACTION11(CHAIN G AND RESID 1:14)
12X-RAY DIFFRACTION12(CHAIN H AND RESID 15:25)
13X-RAY DIFFRACTION13(CHAIN I AND RESID 1:15)
14X-RAY DIFFRACTION14(CHAIN J AND RESID 16:25)
15X-RAY DIFFRACTION15(CHAIN K AND RESID 5:65)
16X-RAY DIFFRACTION16(CHAIN K AND RESID 66:125)
17X-RAY DIFFRACTION17(CHAIN K AND RESID 126:187)
18X-RAY DIFFRACTION18(CHAIN L AND RESID 1:14)
19X-RAY DIFFRACTION19(CHAIN M AND RESID 15:25)
20X-RAY DIFFRACTION20(CHAIN N AND RESID 1:15)
21X-RAY DIFFRACTION21(CHAIN O AND RESID 16:25)

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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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