[English] 日本語
Yorodumi
- PDB-7r4s: Crystal structure of PpSB1-LOV-I48T mutant (dark state) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r4s
TitleCrystal structure of PpSB1-LOV-I48T mutant (dark state)
ComponentsSensory box protein
KeywordsSIGNALING PROTEIN / LOV domain / PAS domain / Photocycle / blue light photoreceptor
Function / homology
Function and homology information


PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGranzin, J. / Batra-Safferling, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Photochem Photobiol Sci / Year: 2023
Title: Residue alterations within a conserved hydrophobic pocket influence light, oxygen, voltage photoreceptor dark recovery.
Authors: Hemmer, S. / Schulte, M. / Knieps-Grunhagen, E. / Granzin, J. / Willbold, D. / Jaeger, K.E. / Batra-Safferling, R. / Panwalkar, V. / Krauss, U.
History
DepositionFeb 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sensory box protein
B: Sensory box protein
C: Sensory box protein
D: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2488
Polymers74,4234
Non-polymers1,8254
Water0
1
A: Sensory box protein
B: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1244
Polymers37,2122
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-35 kcal/mol
Surface area13540 Å2
2
C: Sensory box protein
D: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1244
Polymers37,2122
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-41 kcal/mol
Surface area13780 Å2
Unit cell
Length a, b, c (Å)101.416, 72.146, 91.715
Angle α, β, γ (deg.)90.000, 90.178, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
Sensory box protein


Mass: 18605.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: mutation: I48T / Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
Gene: PP_4629 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88E39
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M sodium chloride, 0.1 M MES pH 6.0, 15 % (v/v) pentaerythritol propoxylate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2018
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→45.86 Å / Num. obs: 17276 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 72 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.082 / Rrim(I) all: 0.192 / Net I/σ(I): 3.4
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2502 / CC1/2: 0.705 / Rpim(I) all: 0.445 / Rrim(I) all: 0.999 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
MxCuBE3data collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J3W

5j3w


Resolution: 2.75→36.19 Å / SU ML: 0.4443 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.0905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2785 798 4.67 %
Rwork0.2289 16282 -
obs0.2313 17080 98.25 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.48 Å2
Refinement stepCycle: LAST / Resolution: 2.75→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 0 124 0 4416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00114481
X-RAY DIFFRACTIONf_angle_d0.30586051
X-RAY DIFFRACTIONf_chiral_restr0.0365641
X-RAY DIFFRACTIONf_plane_restr0.0025788
X-RAY DIFFRACTIONf_dihedral_angle_d13.38461699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.920.43891250.34262640X-RAY DIFFRACTION96.01
2.92-3.150.37281370.33942677X-RAY DIFFRACTION97.74
3.15-3.460.33821140.2842724X-RAY DIFFRACTION98.47
3.46-3.970.32231190.2562748X-RAY DIFFRACTION99.2
3.97-4.990.2491530.20832708X-RAY DIFFRACTION99.24
5-36.190.24041500.18422785X-RAY DIFFRACTION98.82
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)
13.406771097521.331971521692.472743747383.506097565290.9868157952464.322157077560.0351020139551-0.05893608063020.649053316768-0.01550418376050.09791497974220.0471751985965-0.2594688627730.236039936228-0.2878584088490.6775088488420.13306773465-0.05488401924630.7115499469830.03922162489810.83403989841730.07982775787.06245338442.32711460926
23.93512123905-0.3382725327881.684780430518.67264490715-0.2368452326714.081194732390.194151021264-1.10302578772-0.467962430622-0.346747436455-0.314979527209-1.81300987561-0.004247592590010.4979408109870.1282197378270.8146303505420.160593060610.07592572409171.26984378470.05192311306471.2595151854843.14167000380.18858371714910.9842129493
31.15691683599-0.144100113931-1.220200204892.561579644771.620500001654.63710070617-0.273032785659-0.6150328998310.368431856610.4953843287560.609637124227-0.5247301996350.435441764749-0.481455068467-0.4832413550020.5191771125010.245537072832-0.005216657734420.763439029989-0.1053641377950.95636678950933.27874662511.698066208335.55547977559
46.962737825885.661425977172.842225666966.647608758380.5624657651212.762999875452.194061443910.373888738556-0.772512996222-0.116104428694-2.44884855742-1.754155741791.10090241245-1.80475243914-0.7616664953721.666792990090.442756460955-0.2906534669861.40514355474-0.2310187101071.2095497827933.7279488977.8029472805330.8798938463
50.19858537471.00505567924-0.3870623936976.01017633704-1.882988949370.8581311394262.40961071556-4.147670564443.060099231210.800697441992-2.4832799604-1.88726724678-0.693940089921-1.65337824565-0.1154363383681.00480874625-0.209424626847-0.2045309027841.44100392908-0.2164003926081.2277413398540.59520366783.478446501286.20509404985
64.982338004540.1930150589190.5686053848442.737155097561.815449366363.690173259460.544399695816-0.195115147543-0.869103476789-0.174373956894-0.276165573912-0.2239232091220.1104168492190.73416015223-0.1594605497550.718524438430.11288673917-0.1186854510890.6338295581850.00450149900570.78546508846614.579977899-4.741707663765.98742070187
74.823559837063.01242370279-1.320588863542.7108414532-1.354979765594.66649596186-0.809506698692-0.71510220492-0.977388482510.0100273193466-0.298564884327-0.7081560230220.7379035988520.35474362713-0.1597868553280.5920323563211.67305815464-0.231107430663-0.0586878333993-0.2412224872120.86338803915919.269235381-10.400865857915.0015039699
83.19192776781-0.9345468270630.8771347125185.75550842567-2.513014652724.97556180687-0.378820731205-0.455484096164-0.7940714302940.9399728528180.2108089794250.07985683391451.554703921450.3826880580610.4159593044811.080847213160.07034929438210.02481140514530.960536843410.1504319838690.8849363277977.55294080792-9.0394372132319.4194851622
97.97902687632-0.4528741937792.36682466962.98168863033-0.07928010505826.2363478996-0.81890942812-0.2684180385791.41636878361.09479402543-0.03527879474160.714413433744-0.598369079316-0.5519549431840.336615642930.7046311531180.1061240156460.1269162221780.3437288856470.11184315530.664475016452.493343162725.5524889043818.1323989891
105.56780465241-1.58198702561-0.1658342685773.159667912922.619276517584.64699652548-0.669738374249-1.038532719510.257580710041.083882047060.756429710084-0.454916908882-0.9989871062880.1447147780550.01981851088460.8422982715320.1111914954780.08915828215570.847649593119-0.02564654902990.793664287229.766299114044.2308985152819.5180791595
111.10901038691-0.0715126645070.5098572445662.085556658932.898676921674.65528955402-0.346988417496-0.357608170650.2190133820480.7435997795920.332599386517-0.2241920908560.821529198415-0.357226600836-0.03699240165040.7314507228820.164847463433-0.05479394599070.7081323363020.01201140648980.82093815060913.6394856228-2.4001551239418.1469370078
121.85326284909-0.1629442280331.229662603031.721898085950.06563578531532.964807088670.202321553173-0.00902870076051-0.4497148087040.06473134500710.0322261243463-0.1375543545251.15490964490.330797982768-0.2626561842890.7372250307510.1280557137580.09414488374850.527149843665-0.0029536152090.7142195283519.86695198271-0.1135429839576.42350303266
133.772006382853.475433667994.120638841976.004831993734.559826641964.763145905450.9056450102440.967231203828-1.406754844981.717921959930.320444201423-1.600315151732.028170327723.18356380326-1.211966557311.578462329970.122114017517-0.1825731823931.089983615110.1282775983680.84360402851225.46272799064.8962676788434.5640420796
142.40071313457-1.16887387896-0.8590342018272.20516883764-1.371813798682.253579538610.803606152255-1.16364945083-1.947904949741.33595858576-1.297357507940.3942590079242.407537354981.174313716890.8306831702721.34491521671-0.0976897310972-0.1413639156311.12946056844-0.04953203146421.075373903056.22503083115-2.0072209429417.6826462998
158.797089000810.142279226849-4.013651758435.87245824192-3.885351089534.44676445879-0.9137373944280.04646388554970.345037385585-2.273681396571.03218218997-1.055232116191.126666910070.07543611171630.481085935531.007701760370.0155010249833-0.08705221253080.92474338551-0.01624267813340.819973706241.2538221906727.303039611817.8040063981
165.699157916781.479995951281.377388333737.313708829562.654769904841.18353128726-0.111369667013-0.130451057598-0.303181603664-0.6660142009680.1707038940010.453093749668-0.540637594495-0.980718804672-0.08028568897820.9346356805250.133938204937-0.0877466100831.523538972790.1501141088090.792913300709-13.17579375113.708316248922.4871191646
170.165707377147-0.15124830294-0.2191034076098.509584857235.417856133443.547907718960.8517956542060.666945955706-0.88943955451-0.551775288248-2.61326143864-0.2026728829910.952528721646-1.300197186592.833717072741.473652885810.0379948387607-0.001740850684661.695224591440.2729159342411.31046027915-17.87795587512.911160125135.5516351761
182.694503835921.55355086692.546224415367.98894888615-4.229017814937.01638091904-0.9178120922690.0644717039761-1.002259799791.604676872711.411573466630.754900408705-0.798090125866-0.722462702860.516920424690.6216813050890.3467357087130.2027718061281.760945921890.02320548142111.28824393357-18.934861815314.926843723138.9560577251
195.536659989030.231033005803-0.5904016999574.79061819224.372056325376.11474546756-0.89826441587-1.61372872973-0.5989178259920.2100468820431.111868078890.4005597289290.3040297928150.117816257475-0.1241021528770.7443451893550.272645018870.08499271984831.093748275410.2206191026790.656851576417-10.057497608410.637335674333.2844980881
205.296814782951.25430468003-3.343172684532.379347478890.4749720016022.8807615581-2.471868503062.949009249570.948516155613-2.180152930911.117254230120.140639517387-1.23780066066-1.26268276222-0.4316903408831.995553329140.450368125634-0.3813449516081.95033791062-0.1975189045821.40191252-18.639125982631.850663218226.1235596012
215.700846823472.46202319971-1.614013606383.956888020390.9740553981472.32643553576-0.58316901688-1.99492827632-1.83452335881.838797886240.06649840247590.694470816597-0.826220960038-0.03067087130640.1463729681760.6719001622320.4388546089820.1683912390231.299905380430.1050076114110.721827132313-8.2642532821316.766785443129.8499024649
224.6247181327-0.6090003921850.9420820948645.26675312024-0.05958618452481.347596616341.24925596126-0.2099829586490.623354093480.672291463019-0.593591103739-0.798038732958-0.367084365887-1.964216767550.07622661121661.388428102690.340841015718-0.02949245797271.420815215380.3355216291181.042084882954.0281283972-0.97420543677941.705629317
231.71028914242-1.14546406229-0.4938995509722.4656665285-0.7241718040950.787828926912-0.401266010944-1.04203468517-0.280226321049-0.227734958377-0.1711641379630.654881719979-0.225831879299-0.261781534992-2.793586837690.5227208176210.819029960415-0.3306239864543.661371650550.7458609732761.08973470263-16.683647118412.554633381531.4173324395
243.58410693722.890635836491.017136309213.56286427232-0.4092173787123.474524801040.2832787855570.08743241229451.013346057460.123179992642-0.3748725092650.352169527947-0.4078392631390.3874122557810.09380182876870.8138745348450.195915844612-0.0235172836090.687366515403-0.02441977229580.9360323142383.1283872548827.826530199223.0579161537
252.61788983114-1.889903199220.8545586207912.094334340851.979738849869.2506566267-0.166354526267-3.870517082940.4312469158642.445591690350.3766955791660.912839363618-0.268984242955-0.508867570583-0.09060281264091.230618946530.05350504062890.171667864241.043641929870.008945979885310.9236534789925.8817153477426.562004342435.2507980696
261.236560217771.695209131371.196480975626.30117665419-1.960960125847.21364155439-0.331785494604-0.029043462024-0.190842020091.68276667737-0.8849426115151.30462547617-1.98355598582-1.136698988380.8602192788231.189861636490.192230986909-0.1147149128121.07885795332-0.1114486404070.98920138657414.214272984231.864093694131.4235798815
272.962714786860.970391892157-0.865811803733.409718472110.6982896874247.211829131940.10144439822-0.355675442218-0.260988455460.7224794794860.340274596698-0.502377709010.6563242936340.6831222730510.04531589711990.6545919370850.04930711347-0.1088506068841.009282477070.04086286183211.0280878352123.004546595818.163379538425.7419474254
283.796168282962.22917683540.7006855232336.83052427033-0.5378601146815.463522585030.00616394029583-0.515125036525-0.474285114350.4827496863880.35416022168-0.8982955906371.397543706970.4438543625990.1939020270950.7771080341190.290364551443-0.09688478366860.9728824889310.06064172833450.7660120673315.926552234615.815670919127.5275506717
293.77593809609-0.4368031837090.8098499653324.06777925406-1.069204875896.78363810391-0.882413993955-0.6522146135620.3747407450390.3970679809890.0786665462787-0.11017621899-0.739579048550.5416743572010.3165817054210.7140482853970.1440111284610.08515353140020.7325187002130.0007467935698970.71804676554112.117356541920.84038989530.1533445083
304.874763260651.764994464830.4536383790153.18576559001-2.034869102264.106232268260.185998606787-0.736657209098-0.5670647213450.4404276791440.6922544432730.7385290892470.0973575538264-0.321386080437-0.3629289979820.8052809037420.177112500190.0768909743920.889556811661-0.06405316381880.79035998025510.555219249815.518935641829.4056293269
318.692325650583.122910868480.5768974038121.209004762110.4254098254515.32235010991-0.7720940581090.213539656578-1.24566946524-1.17334824955-0.1278078873892.33641850935-0.6409598282311.331213017051.095658361041.281710773990.30674410004-0.05828287830760.8018888428180.02311207688731.2721494740718.22917408222.968874247326.278226266
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 57 )AA2 - 571 - 56
22chain 'A' and (resid 58 through 86 )AA58 - 8657 - 85
33chain 'A' and (resid 87 through 119 )AA87 - 11986 - 118
44chain 'A' and (resid 120 through 132 )AA120 - 132119 - 131
55chain 'A' and (resid 500 through 500 )AB500
66chain 'B' and (resid 2 through 33 )BC2 - 331 - 32
77chain 'B' and (resid 34 through 41 )BC34 - 4133 - 40
88chain 'B' and (resid 42 through 64 )BC42 - 6441 - 63
99chain 'B' and (resid 65 through 74 )BC65 - 7464 - 73
1010chain 'B' and (resid 75 through 86 )BC75 - 8674 - 85
1111chain 'B' and (resid 87 through 104 )BC87 - 10486 - 103
1212chain 'B' and (resid 105 through 119 )BC105 - 119104 - 118
1313chain 'B' and (resid 120 through 133 )BC120 - 133119 - 132
1414chain 'B' and (resid 500 through 500 )BD500
1515chain 'C' and (resid 1 through 12 )CE1 - 121 - 12
1616chain 'C' and (resid 13 through 56 )CE13 - 5613 - 56
1717chain 'C' and (resid 57 through 64 )CE57 - 6457 - 64
1818chain 'C' and (resid 65 through 74 )CE65 - 7465 - 74
1919chain 'C' and (resid 75 through 102 )CE75 - 10275 - 102
2020chain 'C' and (resid 103 through 110 )CE103 - 110103 - 110
2121chain 'C' and (resid 111 through 119 )CE111 - 119111 - 119
2222chain 'C' and (resid 120 through 133 )CE120 - 133120 - 133
2323chain 'C' and (resid 500 through 500 )CF500
2424chain 'D' and (resid 0 through 33 )DG0 - 331 - 34
2525chain 'D' and (resid 34 through 41 )DG34 - 4135 - 42
2626chain 'D' and (resid 42 through 56 )DG42 - 5643 - 57
2727chain 'D' and (resid 57 through 75 )DG57 - 7558 - 76
2828chain 'D' and (resid 76 through 86 )DG76 - 8677 - 87
2929chain 'D' and (resid 87 through 104 )DG87 - 10488 - 105
3030chain 'D' and (resid 105 through 132 )DG105 - 132106 - 133
3131chain 'D' and (resid 500 through 500 )DH500

+
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