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- PDB-3wsf: Oxidized HcgD from Methanocaldococcus jannaschii with citrate -

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Basic information

Entry
Database: PDB / ID: 3wsf
TitleOxidized HcgD from Methanocaldococcus jannaschii with citrate
ComponentsPutative GTP cyclohydrolase 1 type 2
KeywordsMETAL BINDING PROTEIN / NIF3-related protein
Function / homologyNIF3 (NGG1p interacting factor 3)-like / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / CITRIC ACID / :
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
CitationJournal: Febs Lett. / Year: 2014
Title: A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis
Authors: Fujishiro, T. / Ermler, U. / Shima, S.
History
DepositionMar 13, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_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: Putative GTP cyclohydrolase 1 type 2
B: Putative GTP cyclohydrolase 1 type 2
C: Putative GTP cyclohydrolase 1 type 2
D: Putative GTP cyclohydrolase 1 type 2
E: Putative GTP cyclohydrolase 1 type 2
F: Putative GTP cyclohydrolase 1 type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,01518
Polymers169,5276
Non-polymers1,48812
Water22,7711264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15420 Å2
ΔGint-135 kcal/mol
Surface area60410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.190, 137.250, 160.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Putative GTP cyclohydrolase 1 type 2 / HcgD / GTP cyclohydrolase I


Mass: 28254.553 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: MJ0927 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1264 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE HAS ALREADY BEEN DEPOSITED GENBANK, NP_247922. N-TERMINAL RESIDUE, GLY (-2), SER (-1), ...THE SEQUENCE HAS ALREADY BEEN DEPOSITED GENBANK, NP_247922. N-TERMINAL RESIDUE, GLY (-2), SER (-1), HIS(0), ARE THE EXPRESSION TAGS.

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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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10%(w/v) PEG4000, 10%(v/v) 2-propanol, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2012
RadiationMonochromator: Si(111) monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 141911 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.11 % / Biso Wilson estimate: 24.37 Å2 / Rmerge(I) obs: 0.109 / Χ2: 1.034 / Net I/σ(I): 11.08
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.10.8330.7352.677706419201191460.84499.7
2.1-2.30.4310.4274.7212387429160290620.48599.7
2.3-2.80.2090.2078.4217273241564414240.23699.7
2.8-3.30.0860.09314.458258020214201380.10799.6
3.3-4.30.0440.05620.687093317556174440.06499.4
4.3-5.90.0330.04424.6534123898188490.05198.5
5.9-80.0310.04126.2913761347834420.04799
8-120.0230.03130.35926168816550.03798
120.0190.02932.6628747837510.03495.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FYW
Resolution: 2→45.778 Å / FOM work R set: 0.8549 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 7111 5.01 %RANDOM
Rwork0.1777 ---
obs0.1796 141838 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.62 Å2 / Biso mean: 29.73 Å2 / Biso min: 11.06 Å2
Refinement stepCycle: LAST / Resolution: 2→45.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11689 0 84 1264 13037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811987
X-RAY DIFFRACTIONf_angle_d1.10516172
X-RAY DIFFRACTIONf_chiral_restr0.051856
X-RAY DIFFRACTIONf_plane_restr0.0052050
X-RAY DIFFRACTIONf_dihedral_angle_d14.1384492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.33922460.303444524698100
2.0227-2.04650.32792250.281144554680100
2.0465-2.07140.33022270.263144774704100
2.0714-2.09770.26552680.246543754643100
2.0977-2.12530.26612410.222644724713100
2.1253-2.15440.27052160.21454466468299
2.1544-2.18520.24722330.211844344667100
2.1852-2.21780.2222600.197744554715100
2.2178-2.25240.23552380.199744734711100
2.2524-2.28940.25162520.189844484700100
2.2894-2.32880.23162050.195444874692100
2.3288-2.37120.26122250.193644864711100
2.3712-2.41680.21462290.190244514680100
2.4168-2.46610.22832450.184644654710100
2.4661-2.51970.22312240.178145204744100
2.5197-2.57830.23472260.177744764702100
2.5783-2.64280.23292120.18644492470499
2.6428-2.71430.22012270.180444634690100
2.7143-2.79410.22892520.184844924744100
2.7941-2.88430.23812320.190544784710100
2.8843-2.98740.21672310.173445074738100
2.9874-3.10690.22482420.177644674709100
3.1069-3.24830.2092180.177145204738100
3.2483-3.41950.22552420.17664535477799
3.4195-3.63370.19832810.177244674748100
3.6337-3.91410.19912300.15854533476399
3.9141-4.30770.16462310.1414544477599
4.3077-4.93040.14732420.12664496473898
4.9304-6.20940.20482730.1594569484299
6.2094-45.78970.18022380.16274772501098
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)
12.9297-0.49090.40282.7075-0.26061.80830.0713-0.0471-0.3444-0.0250.04420.16820.2682-0.2733-0.10040.1471-0.0352-0.010.1661-0.00620.157-11.8493-113.7966-72.3971
21.1247-1.2691-0.60543.52560.26911.29670.0397-0.17170.10480.05190.0284-0.05160.0537-0.1277-0.08350.1578-0.0055-0.00240.2094-0.01540.1794-11.8436-101.6121-67.9555
33.2190.14550.15981.27360.59661.79370.09980.0647-0.69150.00630.1804-0.22670.44640.1466-0.22390.25870.0681-0.08080.1267-0.07530.350613.4236-120.6775-69.3395
43.54760.69111.75470.62370.40941.60840.13930.136-0.29170.05660.0022-0.10310.17480.0954-0.09610.18570.0251-0.01260.1198-0.04590.200712.912-112.1599-69.5747
51.4225-0.2779-0.18562.82290.91062.81260.01110.0390.335-0.0130.1058-0.2374-0.34880.3518-0.11860.2259-0.08860.03620.2166-0.03970.2463-19.1948-79.7074-57.9921
63.38690.2016-0.80672.6281-0.65831.72740.16940.3040.218-0.1893-0.0186-0.1043-0.37250.1697-0.09180.2508-0.03510.01330.199-0.02320.1579-26.014-85.0849-66.2857
73.03950.46640.35524.1071-1.62573.5117-0.07680.1722-0.0786-0.15290.1510.12850.0077-0.249-0.01070.14820.00150.01140.1956-0.05110.1622-31.5522-90.9932-64.7483
81.9139-1.2125-0.88393.45311.20341.1281-0.0048-0.00470.05530.06420.0693-0.03720.06650.2376-0.06340.1606-0.02350.00920.2084-0.01240.1332-21.3718-95.9311-61.4404
92.5758-0.3638-0.6881.2822-0.66172.9755-0.0072-0.2720.38680.21550.15470.1384-0.5932-0.0341-0.12360.31290.03930.02120.1499-0.04980.2233-32.1688-77.193-38.1344
101.556-0.17140.31362.4751-0.92671.9198-0.0846-0.27160.08980.31960.1640.1791-0.1722-0.1382-0.04270.28720.03570.0250.2547-0.01040.1839-35.511-85.1713-31.9297
112.98850.0472-0.68884.98181.17632.69730.0489-0.33990.01680.11880.0268-0.2745-0.13510.1586-0.03820.22480.02590.00310.2212-0.01060.1413-26.7663-87.4803-31.1015
121.1282-0.16010.60641.6072-0.4492.6564-0.0292-0.3038-0.18410.18360.14180.02770.0459-0.0075-0.03140.21160.02820.01070.24230.02340.1669-31.132-93.2174-28.7301
131.24470.3865-0.22282.0928-0.21151.65830.01910.0270.0902-0.1154-0.05180.1281-0.16260.02010.04150.20920.02520.0210.1651-0.01230.1682-34.2836-80.7143-55.8372
142.59770.96620.63732.770.23471.4729-0.07450.00030.26520.02810.0140.1628-0.1349-0.26270.05570.1490.02810.00610.26710.04730.1894-7.9438-88.7156-9.4055
153.57770.05711.27650.93540.43512.4837-0.05190.21850.3702-0.16780.05-0.0572-0.2992-0.0096-0.01150.28360.0207-0.00750.18520.08160.281712.5119-77.3325-16.6837
161.9356-0.9772-0.07812.21381.24292.7996-0.02510.17970.06620.0593-0.0083-0.1227-0.14270.12490.03280.1698-0.0172-0.00070.1670.0490.189723.5872-87.1283-15.8254
172.0378-0.1542-0.51022.3606-0.14270.98690.00090.01660.17650.1759-0.04540.0354-0.2095-0.06340.060.15930.0136-0.02430.14560.01470.1463.1573-81.5647-2.8591
181.3573-0.5530.1292.16250.27952.5697-0.0663-0.2545-0.21120.15050.03250.01090.2630.04840.00870.1676-0.02460.00420.26290.0480.168-23.4298-113.2331-15.1185
191.55461.30850.43283.1851.47670.3542-0.0693-0.0795-0.0071-0.04590.036-0.00760.060.09970.06130.188-0.00940.0090.32720.05640.1746-19.3104-101.411-16.7562
203.6160.01441.38861.363-0.3322.57540.19640.0727-0.2691-0.28730.07270.06020.6165-0.1185-0.20320.3994-0.07430.01470.25770.0060.2815-28.1718-120.6335-36.4532
212.0297-0.2532-0.23512.6593-1.53223.6691-0.14380.1011-0.264-0.21690.10190.0480.317-0.43140.040.1965-0.07960.02310.2249-0.03150.1838-35.1408-110.8328-45.1607
221.0391-0.85720.81.703-0.58342.10640.0875-0.2046-0.25060.1267-0.01280.10890.2727-0.348-0.06680.2293-0.09190.01140.35540.03150.2677-33.7835-115.6872-20.8458
232.1380.8409-0.92592.7411-0.40212.9246-0.24820.0568-0.443-0.15830.1075-0.18620.48570.13560.10790.26660.01660.02180.21320.01470.25230.3274-115.1143-33.8697
241.0554-0.07240.24363.2506-0.82412.3938-0.02790.0036-0.06590.04660.0639-0.06560.05120.1263-0.02910.1564-0.0133-0.00650.22450.00650.169729.6051-104.5147-35.0565
253.0248-0.8137-1.36861.39470.80672.6927-0.2475-0.4232-0.52240.22220.02120.11510.43530.19750.16630.29220.01910.04020.22910.15340.275913.5583-116.1564-10.975
261.71110.3825-1.29360.05230.25871.5422-0.1476-0.2059-0.2640.03980.0573-0.05040.23160.19820.06380.27270.04280.00220.25330.10240.255323.1618-112.6662-16.9278
271.4644-0.79890.07083.5836-0.30292.67840.0009-0.2210.24940.4118-0.0968-0.356-0.49220.14790.08370.23-0.0443-0.04520.1697-0.01720.206128.8667-82.8707-48.3162
284.33230.68560.02155.1471.69362.85990.0850.0331-0.0011-0.1188-0.0185-0.4277-0.04640.3984-0.07440.1393-0.0132-0.00520.20950.03640.164335.8917-92.997-54.8352
290.5192-0.3024-0.27282.909-1.94751.48110.0293-0.1961-0.0085-0.084-0.01890.00660.11630.0007-0.01570.1908-0.0154-0.02650.1865-0.00110.167827.4926-97.3486-47.7994
301.61030.11890.15910.6943-0.81014.27210.0016-0.03870.36240.0651-0.03040.035-0.3675-0.1254-0.00360.23230.0296-0.00120.1142-0.04330.316113.6638-77.4268-63.196
313.10371.1861-0.32042.3173-0.23171.65220.0640.1270.1399-0.0787-0.03680.07-0.0037-0.1178-0.02310.14550.0395-0.00560.1139-0.02420.17068.6713-86.736-73.6444
321.04020.2021.14042.04340.40321.22760.0413-0.03640.141-0.0467-0.1541-0.1591-0.17880.15180.07590.1979-0.03080.00480.17580.02880.230130.0836-82.4279-61.9201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:69 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 70:103 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 104:154 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 155:249 )
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 6:34 )
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 35:52 )
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 53:69 )
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 70:103 )
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 104:154 )
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 155:182 )
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 183:202 )
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 203:220 )
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 221:249 )
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 5:103 )
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 104:135 )
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 136:220 )
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 221:249 )
18X-RAY DIFFRACTION18CHAIN D AND (RESSEQ 3:69 )
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 70:103 )
20X-RAY DIFFRACTION20CHAIN D AND (RESSEQ 104:135 )
21X-RAY DIFFRACTION21CHAIN D AND (RESSEQ 136:220 )
22X-RAY DIFFRACTION22CHAIN D AND (RESSEQ 221:249 )
23X-RAY DIFFRACTION23CHAIN E AND (RESSEQ 4:61 )
24X-RAY DIFFRACTION24CHAIN E AND (RESSEQ 62:103 )
25X-RAY DIFFRACTION25CHAIN E AND (RESSEQ 104:202 )
26X-RAY DIFFRACTION26CHAIN E AND (RESSEQ 203:249 )
27X-RAY DIFFRACTION27CHAIN F AND (RESSEQ 4:52 )
28X-RAY DIFFRACTION28CHAIN F AND (RESSEQ 53:69 )
29X-RAY DIFFRACTION29CHAIN F AND (RESSEQ 70:103 )
30X-RAY DIFFRACTION30CHAIN F AND (RESSEQ 104:135 )
31X-RAY DIFFRACTION31CHAIN F AND (RESSEQ 136:220 )
32X-RAY DIFFRACTION32CHAIN F AND (RESSEQ 221:249 )

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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

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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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