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- PDB-3bjq: CRYSTAL STRUCTURE OF A PHAGE-RELATED PROTEIN (BB3626) FROM BORDET... -

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Basic information

Entry
Database: PDB / ID: 3bjq
TitleCRYSTAL STRUCTURE OF A PHAGE-RELATED PROTEIN (BB3626) FROM BORDETELLA BRONCHISEPTICA RB50 AT 2.05 A RESOLUTION
ComponentsPhage-related protein
KeywordsVIRAL PROTEIN / PHAGE-RELATED PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyphage-related protein like fold / phage-related protein like domain / : / Major capsid protein GpE / Phage major capsid protein E / Alpha-Beta Complex / Alpha Beta / Major capsid protein E / Uncharacterized protein
Function and homology information
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of phage-related protein (NP_890161.1) from Bordetella bronchiseptica at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 7, 2011Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage-related protein
B: Phage-related protein
C: Phage-related protein
D: Phage-related protein
E: Phage-related protein
F: Phage-related protein
G: Phage-related protein
H: Phage-related protein
I: Phage-related protein
J: Phage-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,72133
Polymers349,41310
Non-polymers4,30823
Water24,0681336
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.390, 188.320, 105.150
Angle α, β, γ (deg.)90.000, 106.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111A
121B
131C
141D
151E
161F
171G
181H
191I
201J
211A
221B
231C
241D
251E
261F
271G
281H
291I
301J
311A
321B
331C
341D
351E
361F
371G
381H
391I
401J

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYSAA12 - 6013 - 61
21VALVALLYSLYSBB12 - 6013 - 61
31VALVALLYSLYSCC12 - 6013 - 61
41VALVALLYSLYSDD12 - 6013 - 61
51VALVALLYSLYSEE12 - 6013 - 61
61VALVALLYSLYSFF12 - 6013 - 61
71VALVALLYSLYSGG12 - 6013 - 61
81VALVALLYSLYSHH12 - 6013 - 61
91VALVALLYSLYSII12 - 6013 - 61
101VALVALLYSLYSJJ12 - 6013 - 61
112GLUGLUCYSCYSAA75 - 18976 - 190
122GLUGLUCYSCYSBB75 - 18976 - 190
132GLUGLUCYSCYSCC75 - 18976 - 190
142GLUGLUCYSCYSDD75 - 18976 - 190
152GLUGLUCYSCYSEE75 - 18976 - 190
162GLUGLUCYSCYSFF75 - 18976 - 190
172GLUGLUCYSCYSGG75 - 18976 - 190
182GLUGLUCYSCYSHH75 - 18976 - 190
192GLUGLUCYSCYSII75 - 18976 - 190
202GLUGLUCYSCYSJJ75 - 18976 - 190
213ILEILEARGARGAA209 - 227210 - 228
223ILEILEARGARGBB209 - 227210 - 228
233ILEILEARGARGCC209 - 227210 - 228
243ILEILEARGARGDD209 - 227210 - 228
253ILEILEARGARGEE209 - 227210 - 228
263ILEILEARGARGFF209 - 227210 - 228
273ILEILEARGARGGG209 - 227210 - 228
283ILEILEARGARGHH209 - 227210 - 228
293ILEILEARGARGII209 - 227210 - 228
303ILEILEARGARGJJ209 - 227210 - 228
314GLYGLYPROPROAA237 - 313238 - 314
324GLYGLYPROPROBB237 - 313238 - 314
334GLYGLYPROPROCC237 - 313238 - 314
344GLYGLYPROPRODD237 - 313238 - 314
354GLYGLYPROPROEE237 - 313238 - 314
364GLYGLYPROPROFF237 - 313238 - 314
374GLYGLYPROPROGG237 - 313238 - 314
384GLYGLYPROPROHH237 - 313238 - 314
394GLYGLYPROPROII237 - 313238 - 314
404GLYGLYPROPROJJ237 - 313238 - 314

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Components

#1: Protein
Phage-related protein


Mass: 34941.262 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Species: Bordetella bronchiseptica / Strain: RB50 / NCTC 13252 / Gene: NP_890161.1, BB3626 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7WDF2, UniProt: A0A0H3LS71*PLUS
#2: Chemical...
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1336 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews3/Da)Density % sol (%)Description
12.5451.5THE STRUCTURE WAS SOLVED BY MAD METHOD USING ANOTHER CRYSTAL AT LOWER RESOLUTION. THE CRYSTAL USED FOR REFINEMENT IS NOT ISOMORPHOUS TO THE CRYSTAL USED FOR PHASING. RIGID BODY REFINEMENT OF THE INITIAL MAD MODEL WAS SUFFICIENT TO ORIENT THE MONOMERS IN THE SET USED FOR REFINEMENT.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop5.79NANODROP, 25.1% PEG 200, 5.0% PEG 3000, 0.1M MES pH 5.79, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop6NANODROP, 30.0% PEG 200, 5.0% PEG 3000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.9184
SYNCHROTRONSSRL BL11-120.97916, 0.91162
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDOct 25, 2007Adjustable focusing mirrors in K-B geometry
MARMOSAIC 325 mm CCD2CCDApr 9, 2007Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) Double crystalSINGLE WAVELENGTHMx-ray1
2Single crystal Si(111) bent (horizontal focusing)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979161
30.911621
ReflectionResolution: 2.05→49.147 Å / Num. obs: 216795 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.49 % / Biso Wilson estimate: 33.52 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.24
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.083.780.8471.734704918499.3
2.08-2.150.7121.9747791957599.8
2.15-2.240.582.4830632172999.8
2.24-2.340.4633775232033899.6
2.34-2.470.3424834662175799.8
2.47-2.620.2585.2770712006299.8
2.62-2.820.37.61216532055099.8
2.82-3.10.22711.31546022061499.8
3.1-3.550.11418.41610912093999.8
3.55-4.470.05827.91612502094299.8
4.47-49.1470.04634.11601722110599.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→49.147 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.972 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. CHLORIDE ION AND PEG 200 (PG4) ARE PRESENT IN THE CRYSTALLIZATION/CRYO CONDITIONS. 5. R FREE SET WAS SELECTED USING THIN SHELLS METHOD DUE TO HIGH NON-CRYSTALLOGRAPHIC SYMMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3532 1.6 %THIN SHELLS
Rwork0.186 ---
obs0.186 216789 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.017 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20.1 Å2
2---1.2 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22752 0 262 1336 24350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02223670
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216050
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.97532156
X-RAY DIFFRACTIONr_angle_other_deg0.892339238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75152983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12423.992967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.783153724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.56515134
X-RAY DIFFRACTIONr_chiral_restr0.080.23556
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0226153
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024549
X-RAY DIFFRACTIONr_nbd_refined0.2040.24583
X-RAY DIFFRACTIONr_nbd_other0.1930.216385
X-RAY DIFFRACTIONr_nbtor_refined0.1780.211427
X-RAY DIFFRACTIONr_nbtor_other0.0870.212349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.21368
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.219
X-RAY DIFFRACTIONr_mcbond_it1.491315298
X-RAY DIFFRACTIONr_mcbond_other0.41735976
X-RAY DIFFRACTIONr_mcangle_it2.337523943
X-RAY DIFFRACTIONr_scbond_it4.24489720
X-RAY DIFFRACTIONr_scangle_it5.874118193
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1497TIGHT POSITIONAL0.10.1
2B1497TIGHT POSITIONAL0.130.1
3C1497TIGHT POSITIONAL0.090.1
4D1497TIGHT POSITIONAL0.120.1
5E1497TIGHT POSITIONAL0.10.1
6F1497TIGHT POSITIONAL0.10.1
7G1497TIGHT POSITIONAL0.110.1
8H1497TIGHT POSITIONAL0.10.1
9I1497TIGHT POSITIONAL0.090.1
10J1497TIGHT POSITIONAL0.160.1
1A1689MEDIUM POSITIONAL0.30.5
2B1689MEDIUM POSITIONAL0.350.5
3C1689MEDIUM POSITIONAL0.320.5
4D1689MEDIUM POSITIONAL0.340.5
5E1689MEDIUM POSITIONAL0.370.5
6F1689MEDIUM POSITIONAL0.340.5
7G1689MEDIUM POSITIONAL0.290.5
8H1689MEDIUM POSITIONAL0.380.5
9I1689MEDIUM POSITIONAL0.310.5
10J1689MEDIUM POSITIONAL0.390.5
1A1497TIGHT THERMAL0.531.2
2B1497TIGHT THERMAL0.481.2
3C1497TIGHT THERMAL0.381.2
4D1497TIGHT THERMAL0.51.2
5E1497TIGHT THERMAL0.491.2
6F1497TIGHT THERMAL0.411.2
7G1497TIGHT THERMAL0.481.2
8H1497TIGHT THERMAL0.451.2
9I1497TIGHT THERMAL0.431.2
10J1497TIGHT THERMAL0.541.2
1A1689MEDIUM THERMAL1.393
2B1689MEDIUM THERMAL1.363
3C1689MEDIUM THERMAL1.213
4D1689MEDIUM THERMAL1.43
5E1689MEDIUM THERMAL1.313
6F1689MEDIUM THERMAL1.223
7G1689MEDIUM THERMAL1.363
8H1689MEDIUM THERMAL1.253
9I1689MEDIUM THERMAL1.223
10J1689MEDIUM THERMAL1.443
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 276 -
Rwork0.277 15688 -
all-15964 -
obs--100 %
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)
10.5453-0.0691-0.30920.46350.51871.44970.0008-0.06760.02530.1505-0.04040.06770.2283-0.17910.0396-0.078-0.0279-0.0168-0.0411-0.0254-0.0688-101.737677.1966-10.1837
21.04570.38760.11320.62740.06510.8725-0.0138-0.03370.0580.07440.02420.01420.0987-0.0938-0.0104-0.0194-0.03970.0233-0.1090.0227-0.0996-93.959539.377428.706
30.9405-0.15650.91860.7034-0.56072.4765-0.08050.2961-0.2061-0.03590.03390.05940.11070.05490.0466-0.0507-0.07230.080.1114-0.11570.0367-116.242661.290315.5133
40.4032-0.06380.23151.0701-0.28240.4173-0.0423-0.02480.0451-0.130.0074-0.20680.1032-0.01140.0348-0.0893-0.0130.0661-0.109-0.0122-0.062-70.743565.3526-12.3932
50.0987-0.0940.0160.4347-0.22830.62750.0439-0.0392-0.05140.0554-0.0329-0.20120.15570.0684-0.011-0.055-0.0105-0.0098-0.09730.0008-0.0122-66.047842.131112.3116
61.5692-0.6950.31131.2177-0.53560.2827-0.1220.00160.15710.38480.007-0.1872-0.25750.09710.1150.0666-0.0694-0.03790.01560.07390.0091-86.806987.854465.9634
71.26410.3403-0.14870.673-0.0510.6350.05910.0081-0.03180.0953-0.04570.0178-0.1330.0048-0.0135-0.0457-0.0261-0.0515-0.0504-0.0182-0.0688-55.132881.890757.9547
81.4078-0.629-0.21340.6770.08890.4594-0.0785-0.0319-0.00930.18950.0835-0.0325-0.02760.0521-0.0050.01550.0279-0.0019-0.0879-0.0141-0.0776-72.8221119.236522.6587
90.1131-0.15810.12060.49490.06230.87080.00260.00260.0268-0.0620.0636-0.04-0.14760.0218-0.0661-0.0533-0.01980.0128-0.0261-0.05040.0094-45.7337101.336631.2229
100.29070.02250.16580.97910.39591.57620.0082-0.0667-0.01990.04260.1022-0.01650.045-0.0231-0.1104-0.08610.04690.0264-0.0731-0.0097-0.1018-97.5631112.194343.8828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 3149 - 315
2X-RAY DIFFRACTION2BB8 - 3149 - 315
3X-RAY DIFFRACTION3CC8 - 3149 - 315
4X-RAY DIFFRACTION4DD8 - 3159 - 316
5X-RAY DIFFRACTION5EE8 - 3159 - 316
6X-RAY DIFFRACTION6FF8 - 3159 - 316
7X-RAY DIFFRACTION7GG8 - 3159 - 316
8X-RAY DIFFRACTION8HH8 - 3149 - 315
9X-RAY DIFFRACTION9II8 - 3159 - 316
10X-RAY DIFFRACTION10JJ8 - 3159 - 316

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