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- PDB-1npb: Crystal structure of the fosfomycin resistance protein from trans... -

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Basic information

Entry
Database: PDB / ID: 1npb
TitleCrystal structure of the fosfomycin resistance protein from transposon Tn2921
Componentsfosfomycin-resistance protein
KeywordsTRANSFERASE / manganese binding / potassium binding loop
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / response to antibiotic / metal ion binding / cytoplasm
Similarity search - Function
2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Glutathione transferase FosA
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPakhomova, S. / Rife, C.L. / Armstrong, R.N. / Newcomer, M.E.
CitationJournal: Protein Sci. / Year: 2004
Title: Structure of fosfomycin resistance protein FosA from transposon Tn2921.
Authors: Pakhomova, S. / Rife, C.L. / Armstrong, R.N. / Newcomer, M.E.
History
DepositionJan 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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.end_auth_comp_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: fosfomycin-resistance protein
B: fosfomycin-resistance protein
C: fosfomycin-resistance protein
D: fosfomycin-resistance protein
E: fosfomycin-resistance protein
F: fosfomycin-resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,45423
Polymers95,8496
Non-polymers1,60517
Water6,269348
1
A: fosfomycin-resistance protein
B: fosfomycin-resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4227
Polymers31,9502
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-88 kcal/mol
Surface area12840 Å2
MethodPISA
2
C: fosfomycin-resistance protein
D: fosfomycin-resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5188
Polymers31,9502
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-103 kcal/mol
Surface area12760 Å2
MethodPISA
3
E: fosfomycin-resistance protein
F: fosfomycin-resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5148
Polymers31,9502
Non-polymers5646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-86 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.597, 208.597, 136.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F
131A
141B
151C
161D
171E
181F
191A
201B
211C
221D
231E
241F
251A
261B
271C
281D
291E
301F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETCYSCYS3AA1 - 421 - 42
21METMETCYSCYS3BB1 - 421 - 42
31METMETCYSCYS3CC1 - 421 - 42
41METMETCYSCYS3DD1 - 421 - 42
51METMETCYSCYS3EE1 - 421 - 42
61METMETCYSCYS3FF1 - 421 - 42
72TRPTRPTYRTYR3AA46 - 5746 - 57
82TRPTRPTYRTYR3BB46 - 5746 - 57
92TRPTRPTYRTYR3CC46 - 5746 - 57
102TRPTRPTYRTYR3DD46 - 5746 - 57
112TRPTRPTYRTYR3EE46 - 5746 - 57
122TRPTRPTYRTYR3FF46 - 5746 - 57
133SERSERTRPTRP5AA63 - 9263 - 92
143SERSERTRPTRP5BB63 - 9263 - 92
153SERSERTRPTRP5CC63 - 9263 - 92
163SERSERTRPTRP5DD63 - 9263 - 92
173SERSERTRPTRP5EE63 - 9263 - 92
183SERSERTRPTRP5FF63 - 9263 - 92
194SERSERGLYGLY5AA101 - 117101 - 117
204SERSERGLYGLY5BB101 - 117101 - 117
214SERSERGLYGLY5CC101 - 117101 - 117
224SERSERGLYGLY5DD101 - 117101 - 117
234SERSERGLYGLY5EE101 - 117101 - 117
244SERSERGLYGLY5FF101 - 117101 - 117
255ALAALAPHEPHE5AA120 - 136120 - 136
265ALAALAPHEPHE5BB120 - 136120 - 136
275ALAALAPHEPHE5CC120 - 136120 - 136
285ALAALAPHEPHE5DD120 - 136120 - 136
295ALAALAPHEPHE5EE120 - 136120 - 136
305ALAALAPHEPHE5FF120 - 136120 - 136

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Components

#1: Protein
fosfomycin-resistance protein


Mass: 15974.843 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: TN2921 / Plasmid: pET-20 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q56415
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 3.87 Å3/Da / Density % sol: 68.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulfate, 100 mM sodium citrate, 5% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
20.6 mM1dropMnCl2
30.6 mMfosfomycin1drop
41.6 Mammonium sulfate1reservoir
5100 mMsodium citrate1reservoirpH6.5
65 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 23, 2002
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL MONOCHROMATOR, BENT CYLINDRICAL SI-MIRROR (RH COATING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 51262 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 50.36 Å2 / Rsym value: 0.082 / Net I/σ(I): 20.5
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 4613 / Rsym value: 0.442 / % possible all: 90.3
Reflection
*PLUS
Lowest resolution: 12 Å / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 90.3 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LQO
Resolution: 2.5→12 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.369 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.23044 1433 3 %RANDOM
Rwork0.18318 ---
obs0.18457 46761 93.79 %-
all-46761 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6602 0 92 348 7042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216874
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9429357
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.21005
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025263
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.22986
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2435
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7171.54130
X-RAY DIFFRACTIONr_mcangle_it1.40326591
X-RAY DIFFRACTIONr_scbond_it2.33132744
X-RAY DIFFRACTIONr_scangle_it3.5684.52766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A212tight positional0.050.05
2B212tight positional0.050.05
3C212tight positional0.050.05
4D212tight positional0.050.05
5E212tight positional0.070.05
6F212tight positional0.050.05
1A252medium positional0.20.5
2B252medium positional0.210.5
3C252medium positional0.440.5
4D252medium positional0.370.5
5E252medium positional0.310.5
6F252medium positional0.30.5
1A469loose positional0.615
2B469loose positional0.585
3C469loose positional0.575
4D469loose positional0.575
5E469loose positional0.55
6F469loose positional0.625
1A212tight thermal0.10.5
2B212tight thermal0.10.5
3C212tight thermal0.10.5
4D212tight thermal0.110.5
5E212tight thermal0.120.5
6F212tight thermal0.110.5
1A252medium thermal0.552
2B252medium thermal0.742
3C252medium thermal0.552
4D252medium thermal0.642
5E252medium thermal0.642
6F252medium thermal0.782
1A469loose thermal1.8310
2B469loose thermal1.7610
3C469loose thermal1.7910
4D469loose thermal1.6210
5E469loose thermal1.7210
6F469loose thermal1.4810
LS refinement shellResolution: 2.5→2.562 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 98
Rwork0.25 2652
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)
12.84310.0597-1.05362.0346-0.34573.45210.1360.131-0.1996-0.2091-0.1529-0.08030.1621-0.16740.01680.21130.0581-0.02880.0524-0.00760.003934.978768.60160.8249
275.7924172.59642.1286324.286932.8233215.99210.08590.2472-4.2448-1.5945-1.23730.1011-0.40656.02471.15140.3196-0.08540.04060.2815-0.01730.301639.76186.7188-4.0634
315.053960.050437.31752.28188.408186.7844-0.61292.20121.71240.049-0.8176-3.0697-3.17862.70321.43050.24040.00840.00010.249-0.00760.239940.646275.590113.8647
4610.2795.057-107.5406563.3013117.3278590.83360.01721.9521.2938-1.5141.46680.0508-0.6246-0.6177-1.4840.4143-0.00360.02970.4229-0.05030.417120.689362.05914.8388
52.55030.3555-0.73431.5567-0.39273.58280.08620.16420.2317-0.0912-0.06920.019-0.4614-0.2384-0.01710.25690.07320.00430.0760.01490.043631.989483.94922.8238
6339.8658-138.164122.9814374.0564-420.006200.3837-0.69930.11291.26961.7641-2.41574.96150.828-1.12563.1150.32820.0377-0.00710.3290.09840.337527.170266.32117.4526
716.0153-174.117-17.9069129.3646157.3473137.71961.1415-0.5964-1.0786-0.9994-2.80881.4546-0.0049-1.97951.66730.27230.0382-0.00390.2534-0.02380.243944.389877.941410.5197
81.4751-0.08340.71723.4923-0.91532.19030.12140.2287-0.0996-0.3233-0.1843-0.07590.3320.25530.06290.21130.08770.07890.1182-0.00140.062451.776735.877223.7886
9388.4494-217.56312.4459469.0063188.2041537.90630.2886-1.00011.31610.42431.29173.3902-1.60492.7941-1.58030.3850.0307-0.00420.3804-0.03850.375834.702743.08419.3074
1014.7732-25.2204-58.808672.424-52.315622.5207-1.4102-2.26131.40180.1213-1.0879-0.1154-2.0305-0.81742.49810.24380.00020.01730.24060.00190.246745.097841.054637.1382
11349.2443-40.181786.5681515.5623-49.5367563.9651-0.00761.1688-1.71771.15641.1746-2.4223-1.1002-1.4006-1.1670.39780.0527-0.03040.37730.03210.374556.670821.059527.411
121.919-0.41270.52392.9409-1.16392.81770.0630.0334-0.1954-0.2618-0.04240.39870.3568-0.3026-0.02060.18110.0005-0.01110.0751-0.03360.176435.761334.417825.7526
13-242.759-119.643363.4705-7.37016.7218-14.6226-0.11610.59180.9838-2.0586-3.4206-3.50173.2163-2.9163.53680.23490.00970.06470.21220.06460.195952.911127.07129.8687
14162.584781.6119-1.467677.561570.2824146.49050.1647-0.7766-3.12491.75262.6183-0.7865.1156-1.1221-2.7830.2481-0.02630.00950.2708-0.00040.245243.394645.45534.2207
15635.611630.245161.9185604.7029-41.8451641.47890.00711.57670.57290.1987-0.00641.9650.1982-0.0881-0.00070.43-0.0201-0.03940.42610.0170.424130.648242.687212.2312
163.1467-0.84740.07791.6817-0.24861.74350.0410.2927-0.1266-0.2264-0.0406-0.0054-0.0612-0.1167-0.00040.0412-0.06870.01250.3287-0.0230.03874.338362.275728.1108
17284.886881.3946-181.0023118.8256215.1553267.4326-0.61551.2219-0.95133.37582.05092.4774-4.4261-1.0331-1.43540.29530.00780.03960.3178-0.06590.2969-4.307764.533944.8916
18111.7534-31.4923-0.048332.2144-12.136246.7961.0187-2.47322.53650.54770.17071.9883-2.44940.3351-1.18940.24320.001-0.01460.24610.00370.250514.923268.387638.0786
19532.0605-41.8159-9.8893525.6032129.3146492.16060.171-0.1475-1.0622-0.26621.4234-0.098-0.29860.5773-1.59440.38550.02510.00670.3886-0.05610.394311.401848.689921.4673
204.081-1.14370.51522.132-0.33531.2557-0.0473-0.3728-0.34960.23320.04180.10320.0588-0.19420.00550.0868-0.08740.02280.31230.02820.05563.815757.614643.6764
21378.7448333.5291-510.2524354.55-16.7716385.01420.85183.2347-2.03442.524-4.07850.31796.40391.11993.22670.3481-0.05810.08060.366-0.0330.350812.41655.13926.6275
22106.1021117.23183.327778.2384-16.642520.5734-0.0287-0.7721-0.6419-1.08370.917-0.6567-2.03832.5123-0.88830.2408-0.0001-0.00410.24280.00810.252310.781871.142240.0893
23191.3501114.636-44.7676385.2961259.3742300.0619-0.16770.3931-1.34912.33620.1452-0.49034.08350.63240.02250.292-0.01050.02460.2575-0.00590.266923.941249.040240.7534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1401 - 140
2X-RAY DIFFRACTION2BG4011
3X-RAY DIFFRACTION3AH4021
4X-RAY DIFFRACTION4AI4031
5X-RAY DIFFRACTION5BB1 - 1391 - 139
6X-RAY DIFFRACTION6DJ4041
7X-RAY DIFFRACTION7CK4051
8X-RAY DIFFRACTION8CC1 - 1381 - 138
9X-RAY DIFFRACTION9CL4061
10X-RAY DIFFRACTION10DM4071
11X-RAY DIFFRACTION11FN4081
12X-RAY DIFFRACTION12DD1 - 1371 - 137
13X-RAY DIFFRACTION13EO4091
14X-RAY DIFFRACTION14EP4101
15X-RAY DIFFRACTION15AQ5011
16X-RAY DIFFRACTION16EE1 - 1381 - 138
17X-RAY DIFFRACTION17BR5021
18X-RAY DIFFRACTION18CS5031
19X-RAY DIFFRACTION19DT5041
20X-RAY DIFFRACTION20FF1 - 1381 - 138
21X-RAY DIFFRACTION21EU5051
22X-RAY DIFFRACTION22FV5061
23X-RAY DIFFRACTION23FW5071
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 12 Å / Rfactor Rfree: 0.2304 / Rfactor Rwork: 0.1832
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.672

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