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- PDB-6g1b: Corynebacterium glutamicum OxyR, oxidized form -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6g1b
TitleCorynebacterium glutamicum OxyR, oxidized form
Components(Hydrogen peroxide-inducible genes ...) x 2
KeywordsTRANSCRIPTION / Hydrogen peroxide / redox / transcription factor / LysR
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / FORMIC ACID / NICKEL (II) ION / HYDROGEN PEROXIDE / : / Probable hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.28 Å
AuthorsYoung, D.R. / Pedre, B.P. / Messens, J.M.
Funding support Belgium, Spain, 7items
OrganizationGrant numberCountry
VIB Belgium
IWT Belgium
HerculesHERC16 Belgium
FWOG.0D79.14N Belgium
VUB Strategic Research ProgrammeSRP34 Belgium
Junta de Castilla y LeonLE326U14 Spain
University of LeonUXXI2016/00127 Spain
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural snapshots of OxyR reveal the peroxidatic mechanism of H2O2sensing.
Authors: Pedre, B. / Young, D. / Charlier, D. / Mourenza, A. / Rosado, L.A. / Marcos-Pascual, L. / Wahni, K. / Martens, E. / G de la Rubia, A. / Belousov, V.V. / Mateos, L.M. / Messens, J.
History
DepositionMar 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Hydrogen peroxide-inducible genes activator
B: Hydrogen peroxide-inducible genes activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,61611
Polymers70,0932
Non-polymers5239
Water5,188288
1
J: Hydrogen peroxide-inducible genes activator
B: Hydrogen peroxide-inducible genes activator
hetero molecules

J: Hydrogen peroxide-inducible genes activator
B: Hydrogen peroxide-inducible genes activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,23222
Polymers140,1864
Non-polymers1,04618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area16570 Å2
ΔGint-87 kcal/mol
Surface area54920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.307, 46.186, 116.692
Angle α, β, γ (deg.)90.000, 121.920, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11J
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010J4 - 318
2010B4 - 323

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Components

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Hydrogen peroxide-inducible genes ... , 2 types, 2 molecules JB

#1: Protein Hydrogen peroxide-inducible genes activator


Mass: 35090.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: C0I99_13405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H5I9R9, UniProt: Q8NP91*PLUS
#2: Protein Hydrogen peroxide-inducible genes activator


Mass: 35002.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: C0I99_13405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H5I9R9, UniProt: Q8NP91*PLUS

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Non-polymers , 6 types, 297 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM, PPS


Mass: 201.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3S
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, sodium cacodylate, magnesium acetate, nicotinamide adenine dinucelotide hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.28→46.07 Å / Num. obs: 32352 / % possible obs: 96.6 % / Redundancy: 5.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.059 / Rrim(I) all: 0.134 / Net I/σ(I): 8.1 / Num. measured all: 165386 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.28-2.365.10.9551548930250.690.4591.0621.593.3
8.85-46.074.70.06926995790.9870.0360.07924.691.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.29data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 2.28→99.05 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2195 / WRfactor Rwork: 0.1874 / FOM work R set: 0.8118 / SU B: 14.112 / SU ML: 0.174 / SU R Cruickshank DPI: 0.3322 / SU Rfree: 0.2224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 1589 4.9 %RANDOM
Rwork0.1962 ---
obs0.1979 30760 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 131.62 Å2 / Biso mean: 47.326 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0.4 Å2
2--0.85 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 2.28→99.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4752 0 30 288 5070
Biso mean--59.53 42.93 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194990
X-RAY DIFFRACTIONr_bond_other_d0.0020.024755
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9896820
X-RAY DIFFRACTIONr_angle_other_deg0.959311047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73124.588194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31315830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0951529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215566
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02923
Refine LS restraints NCS

Ens-ID: 1 / Number: 17642 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1J
2B
LS refinement shellResolution: 2.284→2.343 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 110 -
Rwork0.312 2135 -
all-2245 -
obs--91.3 %
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)
14.8898-2.89166.76842.1124-3.92539.40430.60180.0469-0.6628-0.24680.42670.26770.89010.1432-1.02860.4670.0786-0.12240.5872-0.10810.3931123.657946.485717.4109
25.8208-1.29254.86733.9892-4.10226.54420.2488-0.3202-0.13040.1865-0.12490.0840.0381-0.1518-0.12390.3645-0.00490.08330.5306-0.00170.2528109.029955.013121.4717
35.60531.9667-4.96131.7675-0.12127.36880.13290.43090.24170.22020.34570.110.0697-0.3923-0.47860.33020.0647-0.01070.44960.03290.3184104.61863.172511.0811
43.1867-2.3296-0.55424.32471.091.16410.0283-0.2578-0.0179-0.03810.01630.1635-0.04060.0091-0.04460.32920.00050.07360.4383-0.04410.3032112.658460.911217.6545
50.72050.3789-1.09064.34811.69122.8974-0.02940.1427-0.0663-0.36280.0364-0.1245-0.1752-0.2432-0.0070.3120.00030.06310.5137-0.0240.3254110.695857.31156.2174
60.6067-0.7894-1.19811.24540.28689.82910.01080.0338-0.0766-0.0181-0.06730.10760.0063-0.06550.05660.3177-0.03610.00420.42540.01530.3852103.315849.025418.0207
711.9576-4.0868-5.01496.79236.08365.6432-0.1232-0.2463-0.1055-0.27160.1965-0.0856-0.21290.1914-0.07330.256-0.0460.14020.51740.05320.237895.917353.695735.2824
80.6894-0.04750.29090.0921-0.18530.4322-0.0149-0.20880.0409-0.02350.0063-0.00860.0507-0.08670.00860.43170.00550.05490.4799-0.03140.267675.868752.663131.0703
90.8407-2.0613-2.71775.34886.97999.1339-0.0060.0532-0.0950.3853-0.33240.21850.4118-0.40090.33840.493-0.1527-0.01970.5340.04930.297674.872746.49836.246
101.4128-3.0041.1056.5647-2.46180.93540.13320.00050.2122-0.0449-0.2206-0.328-0.04750.13680.08740.5912-0.16670.01110.6386-0.11170.288777.907253.365242.3348
111.29580.89330.20893.1813-0.01230.15190.00820.03070.2128-0.1735-0.03710.06150.0272-0.12330.02880.40530.00490.04790.40350.00050.282972.870657.551122.5393
120.12580.5518-0.02793.52860.44850.3550.0122-0.0029-0.0605-0.19670.0084-0.1676-0.06840.0338-0.02060.37360.01330.07420.38560.02120.338279.941746.615418.9335
132.245-1.56980.06752.8715-0.69460.7255-0.04520.1039-0.0667-0.47830.0228-0.20220.1586-0.0470.02240.48330.02220.08240.3749-0.02750.230575.843927.45597.9305
140.1414-0.0242-0.182.19820.01540.2409-0.0649-0.06530.0164-0.41130.04940.00690.06180.06280.01550.47640.01190.10450.44460.00720.260978.510539.93018.1224
156.15124.13330.568711.13123.83411.48730.2859-0.47740.0677-0.712-0.2869-0.0576-0.3161-0.08490.00090.5728-0.00080.22140.4793-0.01080.235676.581146.17463.3846
161.25441.31360.41581.90222.45187.8837-0.00470.08970.24030.00560.04350.21950.0194-0.057-0.03880.33290.03220.04450.47650.01370.349863.131941.20710.8595
170.76820.21491.04691.10730.62721.72650.0452-0.0431-0.2035-0.03720.00630.02520.03290.0281-0.05150.38570.00980.06750.45630.01770.307268.050534.473918.2994
180.2968-0.1250.38230.8467-0.14980.55240.0426-0.0578-0.0138-0.0164-0.0948-0.18590.00140.01830.05210.3732-0.0060.09880.44290.01470.313378.575243.709420.6267
190.80970.05590.35216.93350.740.6505-0.0177-0.092-0.1480.22640.203-0.29290.0254-0.0517-0.18530.4059-0.025-0.04840.46720.00220.294584.729853.244633.1742
200.6155-0.46480.20571.1368-0.1751.7332-0.0214-0.1056-0.05960.1569-0.0451-0.3133-0.05770.03230.06650.3901-0.00210.04170.44280.05740.308781.522333.661426.1201
210.29031.04350.008410.02883.67122.8563-0.10890.222-0.056-0.2323-0.0745-0.1469-0.1606-0.09910.18330.3186-0.09640.02650.61630.04010.103153.817750.3161-36.2906
2210.902-1.6706-7.20010.56470.015810.1344-0.92690.4549-1.77880.10350.23460.38450.5218-0.48450.69220.4605-0.19440.00950.836-0.03780.439948.462439.5825-45.6861
231.25581.0575-2.467510.10851.60846.35-0.0880.1347-0.1801-0.0863-0.2058-0.19760.0991-0.33490.29380.2486-0.10120.0050.4989-0.07050.299842.185544.6923-40.5182
245.429-0.7603-4.23876.40240.06143.35530.42810.90730.5812-0.87160.0069-0.2624-0.2703-0.6961-0.43490.3446-0.04590.06430.82670.13530.0754.328552.0427-44.2993
2513.697610.6227-0.81458.2405-0.63150.0506-0.28490.38410.1424-0.19370.28010.11810.0217-0.02770.00480.3649-0.05760.07680.6657-0.13890.108854.186241.3499-51.654
261.0717-0.2748-2.8422.10420.986610.0507-0.35360.3356-0.3083-0.14970.0787-0.26220.3884-0.31240.27490.3716-0.10280.23060.5621-0.18520.275862.242744.5047-38.0893
271.8530.1817-2.71960.8392-2.610310.6816-0.27590.0734-0.2694-0.01190.10.0490.3668-0.33030.17590.4081-0.01190.12160.3718-0.0850.272152.616443.7399-24.1075
285.73752.56853.71842.862-0.41154.9374-0.4233-0.1768-0.1257-0.6780.1734-0.35370.3669-0.43870.24990.4581-0.07080.00950.4517-0.0390.314246.694141.5786-14.7857
290.94390.06671.0421.0962-0.21511.3218-0.17430.04920.059-0.05460.06950.0548-0.035-0.08460.10480.3541-0.02250.05310.5034-0.01440.262652.382640.68539.8193
302.80292.39261.6472.59110.72712.1052-0.12840.30330.0172-0.17370.2126-0.09970.0860.1845-0.08420.38880.00680.03210.4606-0.03870.247452.517937.8914.9086
312.3618-0.37834.27650.5401-0.02439.3931-0.26570.00790.0330.03490.0075-0.1687-0.38290.01150.25820.3743-0.01-0.00410.4250.0090.312455.64355.16348.3467
320.59550.8571-0.64052.0153-2.57384.3281-0.0867-0.05540.14480.05650.07270.1845-0.1108-0.16060.0140.35580.0420.0630.4527-0.01160.311745.03551.365514.1062
330.04640.22230.21621.37771.36611.35810.1058-0.04450.03380.3029-0.13690.04990.2728-0.15480.03110.43550.01170.14850.6870.0340.113750.177442.591840.7028
342.0121-0.14432.16650.5631-0.21923.0432-0.3752-0.3142-0.00190.0830.0896-0.0475-0.0411-0.06680.28560.38890.09180.10160.523-0.01580.248551.87251.043134.14
358.482.0587-1.16060.575-0.34940.3394-0.121-0.60261.2282-0.06440.02250.1803-0.07180.06330.09840.40730.0309-0.02040.6195-0.11470.569353.082355.035932.9231
363.5499-4.69561.0856.3888-1.52650.38080.01290.0448-0.059-0.2062-0.058-0.00570.0889-0.0050.04510.39260.00350.02730.4297-0.0340.371462.945543.540629.6315
370.81921.0724-0.69711.7471-0.92830.65610.0781-0.0857-0.11190.1317-0.1615-0.16190.0093-0.09130.08330.3794-0.04490.04030.58820.03320.228256.258339.578533.0672
380.11030.1226-0.3440.5836-1.91216.5498-0.1535-0.07550.0958-0.0184-0.03030.01180.1068-0.18640.18370.37360.054-0.01220.5002-0.06070.336944.273149.811915.1336
390.90950.62582.0024.0984-1.28086.4682-0.1383-0.0050.0347-0.24580.15910.11640.0284-0.1733-0.02080.4166-0.0039-0.02360.40680.00650.350241.433546.23591.9676
400.7210.15641.0140.6020.02213.02150.0618-0.0852-0.0456-0.0582-0.14760.04050.1965-0.20710.08580.32-0.00890.05050.47390.01650.27544.331236.131720.981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B-2 - 6
2X-RAY DIFFRACTION2B7 - 19
3X-RAY DIFFRACTION3B20 - 28
4X-RAY DIFFRACTION4B29 - 52
5X-RAY DIFFRACTION5B53 - 68
6X-RAY DIFFRACTION6B69 - 82
7X-RAY DIFFRACTION7B83 - 92
8X-RAY DIFFRACTION8B93 - 112
9X-RAY DIFFRACTION9B113 - 119
10X-RAY DIFFRACTION10B120 - 129
11X-RAY DIFFRACTION11B130 - 156
12X-RAY DIFFRACTION12B157 - 178
13X-RAY DIFFRACTION13B179 - 197
14X-RAY DIFFRACTION14B198 - 214
15X-RAY DIFFRACTION15B215 - 225
16X-RAY DIFFRACTION16B226 - 237
17X-RAY DIFFRACTION17B238 - 258
18X-RAY DIFFRACTION18B259 - 291
19X-RAY DIFFRACTION19B292 - 303
20X-RAY DIFFRACTION20B304 - 323
21X-RAY DIFFRACTION21J4 - 21
22X-RAY DIFFRACTION22J22 - 28
23X-RAY DIFFRACTION23J29 - 38
24X-RAY DIFFRACTION24J39 - 56
25X-RAY DIFFRACTION25J57 - 65
26X-RAY DIFFRACTION26J66 - 78
27X-RAY DIFFRACTION27J79 - 87
28X-RAY DIFFRACTION28J88 - 93
29X-RAY DIFFRACTION29J94 - 118
30X-RAY DIFFRACTION30J119 - 135
31X-RAY DIFFRACTION31J136 - 149
32X-RAY DIFFRACTION32J150 - 171
33X-RAY DIFFRACTION33J172 - 192
34X-RAY DIFFRACTION34J193 - 209
35X-RAY DIFFRACTION35J210 - 229
36X-RAY DIFFRACTION36J230 - 235
37X-RAY DIFFRACTION37J236 - 266
38X-RAY DIFFRACTION38J267 - 285
39X-RAY DIFFRACTION39J286 - 290
40X-RAY DIFFRACTION40J291 - 318

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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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