[English] 日本語
Yorodumi
- PDB-3enz: Arsenolytic structure of Plasmodium falciparum purine nucleoside ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3enz
TitleArsenolytic structure of Plasmodium falciparum purine nucleoside phosphorylase with hypoxanthine, ribose and arsenate ion
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / CATALYTICALLY-RELEVANT ARSENOLYTIC-INTERMEDIATE-STATE COMPLEX / Glycosyltransferase
Function / homology
Function and homology information


Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / S-methyl-5-thioadenosine phosphorylase activity / inosine catabolic process / uridine catabolic process / guanosine phosphorylase activity / uridine phosphorylase activity / purine-nucleoside phosphorylase ...Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / S-methyl-5-thioadenosine phosphorylase activity / inosine catabolic process / uridine catabolic process / guanosine phosphorylase activity / uridine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / cytosol
Similarity search - Function
Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARSENATE / FORMIC ACID / HYPOXANTHINE / 1,4-anhydro-D-ribitol / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsChaikuad, A. / Brady, R.L.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases.
Authors: Chaikuad, A. / Brady, R.L.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / pdbx_chem_comp_identifier ...atom_site / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.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 / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,44853
Polymers167,7746
Non-polymers3,67547
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20510 Å2
ΔGint-83.4 kcal/mol
Surface area49180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.820, 177.820, 253.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
22A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 43
2224A1 - 43

NCS ensembles :
ID
1
2
DetailsThe hexamer in the asymmetric unit represents the biological unit.

-
Components

-
Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
Purine nucleoside phosphorylase


Mass: 27962.311 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFE0660c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8I3X4, purine-nucleoside phosphorylase
#3: Sugar
ChemComp-R1X / 1,4-anhydro-D-ribitol / 1-deoxyribose


Type: D-saccharide / Mass: 134.130 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H10O4
IdentifierTypeProgram
D-1-deoxy-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 5 types, 599 molecules

#2: Chemical
ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H4N4O
#4: Chemical
ChemComp-ART / ARSENATE


Mass: 138.919 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: AsO4
#5: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4.0M Sodium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.196 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2007
RadiationMonochromator: double crystal Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.196 Å / Relative weight: 1
ReflectionResolution: 2.03→145.86 Å / Num. all: 129248 / Num. obs: 129248 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 18.5
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 8 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.556 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NW4
Resolution: 2.03→145.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.408 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19325 6502 5 %RANDOM
Rwork0.16035 ---
all0.16201 129248 --
obs0.16035 122746 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.879 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.03→145.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11226 0 221 558 12005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02211665
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.98315755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69851471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92524.762483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.305152023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5151554
X-RAY DIFFRACTIONr_chiral_restr0.0980.21805
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028580
X-RAY DIFFRACTIONr_nbd_refined0.1980.25529
X-RAY DIFFRACTIONr_nbtor_refined0.3010.27818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2701
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.216
X-RAY DIFFRACTIONr_mcbond_it0.721.57325
X-RAY DIFFRACTIONr_mcangle_it1.235211744
X-RAY DIFFRACTIONr_scbond_it2.2834424
X-RAY DIFFRACTIONr_scangle_it3.5844.54005
Refine LS restraints NCS

Auth asym-ID: A / Number: 144 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å

Ens-IDDom-IDTypeWeight position
11medium positional0.5
22medium thermal2
LS refinement shellResolution: 2.03→2.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 497 -
Rwork0.195 8953 -
obs--99.62 %
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)
11.72690.5235-1.04171.7027-0.0933.02320.15740.00140.19550.0644-0.0385-0.0675-0.43440.1774-0.11890.2114-0.01450.0729-0.0686-0.00760.014843.499836.820736.7442
20.7029-0.1106-0.25111.64750.03960.72210.0317-0.05320.0290.11060.00920.1302-0.1611-0.0608-0.04080.12060.01780.06780.00280.00180.00937.562322.686238.7313
30.63770.4008-0.3431.17850.17851.80780.06390.076-0.0209-0.0844-0.04860.1995-0.1552-0.23-0.01530.10440.03750.03750.06090.00610.092730.978114.479229.4085
42.67360.091.22831.70210.40382.92750.01090.00070.0597-0.07360.03090.1362-0.1933-0.1488-0.04190.14090.00780.06950.00640.01920.0735.412519.384433.3898
53.5890.78423.49452.17782.892910.95460.0623-0.1080.02720.01570.07910.3055-0.6744-0.17-0.14140.24310.08740.1154-0.01330.01520.118228.738730.486139.4432
61.6103-0.0786-0.73862.2175-0.86452.14930.10660.18160.174-0.03150.0090.1158-0.3461-0.1562-0.11560.18730.03270.0706-0.00780.02120.026144.766233.250712.772
71.2262-0.1652-0.34231.6233-0.4110.70950.03750.0840.0398-0.1921-0.0407-0.217-0.09470.04320.00320.1498-0.00850.08060.048-0.00140.057657.755119.754514.8772
80.93-0.261-0.44470.6565-0.04530.79680.0675-0.08750.0050.0391-0.0525-0.1914-0.13170.1839-0.0150.1362-0.03820.0590.0631-0.0010.099762.735719.496523.6654
91.85910.30970.76631.76830.42972.56630.04110.01320.146-0.0020.0134-0.1372-0.19380.1154-0.05450.1293-0.00970.07480.0004-0.00740.074357.597322.455320.2633
106.93372.71918.03083.01883.676116.08840.10670.20910.1348-0.10330.0431-0.1827-0.3772-0.1201-0.14990.2158-0.00110.1353-0.02850.03990.106858.927133.60939.0826
111.38640.1483-0.88451.6164-0.42071.3043-0.02-0.079-0.16810.0236-0.01640.10050.0472-0.0810.03640.0543-0.0020.06270.03950.03640.070625.5454-9.238353.3857
123.99990.3664-1.03450.48710.4551.44120.1374-0.5392-0.02520.2424-0.1481-0.1135-0.21940.31850.01070.1383-0.03280.01880.13750.02780.035343.78864.911957.9759
130.75480.2535-0.55570.5751-0.08861.09370.0236-0.1033-0.02120.0617-0.03370.0202-0.04760.07560.01010.0855-0.00370.04740.03960.01810.062141.04883.542647.434
141.7799-0.2508-0.98811.16070.07011.108-0.0368-0.4121-0.01980.2232-0.0353-0.0555-0.02260.25010.07210.1419-0.00560.06110.13280.04830.058237.92970.605759.2925
1562.0919-53.2512-15.685169.286626.027342.52461.09851.25831.0903-2.3745-1.3627-1.2046-2.2925-1.93580.26420.16420.15780.00890.1171-0.06090.253513.60857.140250.7029
161.39260.0064-0.72352.3978-0.88183.1009-0.06220.0079-0.1341-0.2023-0.1191-0.40160.11690.23310.18130.0620.01350.14540.0171-0.01130.107377.5587-5.47191.3828
172.3734-0.4941-0.29971.0758-0.08311.2171-0.02590.3042-0.063-0.2118-0.0547-0.0347-0.05360.01290.08060.1308-0.0010.09120.0291-0.02520.053762.9024-0.07644.1541
180.9666-0.1282-0.251.00390.08371.06490.02670.11890.0201-0.1574-0.0274-0.0781-0.0999-0.04640.00070.10450.01350.08230.0324-0.0080.061858.19363.60637.3308
192.27380.0450.18040.7720.33251.65890.0150.2102-0.1638-0.145-0.0396-0.05250.0475-0.06130.02460.1411-0.00620.07530.0252-0.01910.06255.54280.63026.1488
206.69564.72041.42845.46911.08342.19090.01060.1848-0.1234-0.3179-0.1548-0.31270.0175-0.09330.14420.19430.01890.15850.0879-0.03150.033567.0292.0053-6.1861
212.0359-0.1771-0.66373.0431-0.31291.9627-0.1618-0.4039-0.40030.260.0533-0.01190.23290.17050.10860.05380.06340.10970.01270.14070.105645.1571-25.556354.1134
222.34180.13930.76231.12140.06053.3794-0.2025-0.0368-0.3165-0.1452-0.0583-0.04320.3271-0.08610.26080.115-0.00010.1554-0.08270.03270.185242.1766-26.395336.9171
230.88970.2011-0.33240.88090.06581.2598-0.15770.0349-0.249-0.06970.0243-0.01390.19810.01760.13350.10240.00410.0989-0.02790.01340.123644.3886-20.123133.0931
245.45440.39640.98891.412-0.45342.1154-0.1569-0.0588-0.267-0.07140.024-0.01870.1796-0.08170.13290.10310.01660.1293-0.0722-0.01510.090441.6187-22.305136.2984
2510.3133-3.23823.69543.9624-1.68114.2409-0.3693-0.1404-0.3969-0.03480.0860.00980.4896-0.06890.28330.1732-0.02980.2188-0.12560.0490.192739.0721-33.37941.8306
261.7356-0.4437-1.20852.19510.22753.3432-0.15660.1006-0.2344-0.02450.04890.13910.1845-0.00720.10770.0732-0.00440.1489-0.0454-0.05980.112563.5824-26.17254.1069
270.7295-0.2451-0.31770.8890.2851.3155-0.1785-0.0743-0.24760.0110.041-0.07370.24360.16180.13750.10120.04290.1422-0.01910.02510.136962.2089-21.766121.4278
281.62620.3814-0.32161.19350.39361.8505-0.1688-0.0868-0.1376-0.02030.0366-0.19630.11180.29820.13220.07150.050.1184-0.02360.03920.133663.4417-17.664925.0784
2924.5855-22.0073-14.37271.710216.7658.6939-0.8495-1.15420.292-1.14490.9235-2.86960.64590.9911-0.0740.33680.27550.13050.32930.11740.388181.1438-18.388822.6373
3026.54348.06855.99747.42762.67524.1339-0.0505-0.3296-0.7597-0.03940.0729-0.15750.76210.0843-0.02240.21560.0970.2743-0.13210.04240.153266.1684-35.51718.103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 48
2X-RAY DIFFRACTION2A49 - 142
3X-RAY DIFFRACTION3A143 - 183
4X-RAY DIFFRACTION4A184 - 215
5X-RAY DIFFRACTION5A216 - 246
6X-RAY DIFFRACTION6B3 - 80
7X-RAY DIFFRACTION7B81 - 141
8X-RAY DIFFRACTION8B142 - 183
9X-RAY DIFFRACTION9B184 - 217
10X-RAY DIFFRACTION10B218 - 247
11X-RAY DIFFRACTION11C3 - 86
12X-RAY DIFFRACTION12C87 - 109
13X-RAY DIFFRACTION13C110 - 194
14X-RAY DIFFRACTION14C195 - 243
15X-RAY DIFFRACTION15C244 - 248
16X-RAY DIFFRACTION16D3 - 63
17X-RAY DIFFRACTION17D64 - 109
18X-RAY DIFFRACTION18D110 - 168
19X-RAY DIFFRACTION19D169 - 215
20X-RAY DIFFRACTION20D216 - 246
21X-RAY DIFFRACTION21E3 - 77
22X-RAY DIFFRACTION22E78 - 109
23X-RAY DIFFRACTION23E110 - 191
24X-RAY DIFFRACTION24E192 - 213
25X-RAY DIFFRACTION25E214 - 245
26X-RAY DIFFRACTION26F3 - 50
27X-RAY DIFFRACTION27F51 - 170
28X-RAY DIFFRACTION28F171 - 213
29X-RAY DIFFRACTION29F214 - 223
30X-RAY DIFFRACTION30F224 - 245

+
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://pdbjlvh1.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