[English] 日本語
Yorodumi
- PDB-4gzv: Crystal structure of a lipocalin family protein (BACOVA_00364) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gzv
TitleCrystal structure of a lipocalin family protein (BACOVA_00364) from Bacteroides ovatus ATCC 8483 at 1.95 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / An eight-stranded beta barrel / lipocalin family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF4488 / Domain of unknown function (DUF4488) / Uncharacterised protein PF14869 family, DUF4488 / Lipocalin / Beta Barrel / Mainly Beta / ACETATE ION / Unknown ligand / DUF4488 domain-containing protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_00364) from Bacteroides ovatus ATCC 8483 at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Non-polymer description
Revision 1.2Feb 13, 2013Group: Other
Revision 1.3Dec 24, 2014Group: Structure summary
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein
E: hypothetical protein
F: hypothetical protein
G: hypothetical protein
H: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,74919
Polymers132,2998
Non-polymers45011
Water9,998555
1
A: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3939
Polymers66,1494
Non-polymers2435
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-70 kcal/mol
Surface area26290 Å2
MethodPISA
2
E: hypothetical protein
F: hypothetical protein
G: hypothetical protein
H: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,35710
Polymers66,1494
Non-polymers2076
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-77 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.781, 66.323, 109.737
Angle α, β, γ (deg.)88.23, 82.26, 74.75
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A31 - 162
2010B31 - 162
1020A28 - 162
2020C28 - 162
1030A31 - 162
2030D31 - 162
1040A25 - 162
2040E25 - 162
1050A28 - 162
2050F28 - 162
1060A28 - 162
2060G28 - 162
1070A28 - 163
2070H28 - 163
1080B31 - 162
2080C31 - 162
1090B31 - 163
2090D31 - 163
10100B31 - 162
20100E31 - 162
10110B31 - 162
20110F31 - 162
10120B31 - 162
20120G31 - 162
10130B31 - 163
20130H31 - 163
10140C31 - 162
20140D31 - 162
10150C28 - 162
20150E28 - 162
10160C28 - 163
20160F28 - 163
10170C28 - 163
20170G28 - 163
10180C28 - 163
20180H28 - 163
10190D31 - 162
20190E31 - 162
10200D31 - 162
20200F31 - 162
10210D31 - 162
20210G31 - 162
10220D31 - 163
20220H31 - 163
10230E28 - 162
20230F28 - 162
10240E28 - 162
20240G28 - 162
10250E28 - 163
20250H28 - 163
10260F28 - 163
20260G28 - 163
10270F28 - 163
20270H28 - 163
10280G28 - 163
20280H28 - 163

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
hypothetical protein /


Mass: 16537.361 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_00364, ZP_02063416.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7LRD6

-
Non-polymers , 5 types, 566 molecules

#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 5 / Source method: obtained synthetically
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 23-163 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.085M tris hydrochloride pH 8.5, 15% glycerol, 25.5% polyethylene glycol 4000, 0.17M sodium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.9792,0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 3, 2012 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.97921
30.979051
ReflectionResolution: 1.95→29.85 Å / Num. all: 86141 / Num. obs: 86141 / % possible obs: 97.8 % / Redundancy: 2.9 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.087 / Rsym value: 0.071 / Net I/av σ(I): 7.132 / Net I/σ(I): 10.5 / Num. measured all: 250141
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-220.6280.4451.61261762960.4420.6280.4451.896.7
2-2.0630.5490.4471.71815961300.3150.5490.4472.497.1
2.06-2.1230.430.3492.11783660270.2470.430.349397.1
2.12-2.1830.3560.2892.61736558400.2040.3560.2893.697.1
2.18-2.2530.290.2352.21683256700.1660.290.2354.397.5
2.25-2.3330.2490.2033.71630554680.1420.2490.203597.4
2.33-2.4230.2070.1694.41567052650.1190.2070.1695.797.6
2.42-2.5230.1880.1534.91528051200.1070.1880.1536.297.7
2.52-2.6330.1560.1275.81468949260.0890.1560.1277.397.9
2.63-2.7630.1210.0997.11404246960.0690.1210.0999.298
2.76-2.9130.1050.0868.11326144520.060.1050.08610.698.3
2.91-3.0830.0850.0699.91261842350.0480.0850.06913.298.4
3.08-3.330.0710.05810.81190839930.0390.0710.05816.898.5
3.3-3.5630.0590.04912.21106837230.0330.0590.04921.298.8
3.56-3.930.0550.04512.91020734200.0310.0550.04524.898.8
3.9-4.3630.050.04113.6926331090.0280.050.0412898.9
4.36-5.0330.0510.04213.2811227310.0290.0510.04229.599.1
5.03-6.1730.0580.04712681822990.0330.0580.04727.799.2
6.17-8.7230.0620.05111.6534217990.0350.0620.05128.599.2
8.72-29.8492.90.0520.04213.527499420.030.0520.04233.796.1

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.21 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.149
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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 6. SODIUM ION (NA), ACETATE ION (ACT) AND GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 7. AN UNKNOWN LIGAND (UNL) IS MODELED IN CHAINS A, D, E, F, AND G.
RfactorNum. reflection% reflectionSelection details
Rfree0.22034 4305 5 %RANDOM
Rwork0.18883 ---
obs0.19043 81725 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.677 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.9 Å20.29 Å2
2---1.66 Å20.04 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8691 0 74 555 9320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.029073
X-RAY DIFFRACTIONr_bond_other_d0.0080.025985
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.96312372
X-RAY DIFFRACTIONr_angle_other_deg1.755314691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.21551103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.36225.255432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73151483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3391524
X-RAY DIFFRACTIONr_chiral_restr0.1080.21364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110049
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021799
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A45040.13
12B45040.13
21A46450.11
22C46450.11
31A45590.12
32D45590.12
41A47250.12
42E47250.12
51A43190.13
52F43190.13
61A46860.12
62G46860.12
71A43680.11
72H43680.11
81B44440.11
82C44440.11
91B46450.12
92D46450.12
101B44890.12
102E44890.12
111B41580.14
112F41580.14
121B45230.11
122G45230.11
131B41950.12
132H41950.12
141C44530.1
142D44530.1
151C45110.1
152E45110.1
161C42540.12
162F42540.12
171C47200.07
172G47200.07
181C44240.08
182H44240.08
191D44870.11
192E44870.11
201D42830.11
202F42830.11
211D45760.11
212G45760.11
221D43030.09
222H43030.09
231E43740.11
232F43740.11
241E46730.1
242G46730.1
251E43520.09
252H43520.09
261F43560.13
262G43560.13
271F41830.1
272H41830.1
281G44700.08
282H44700.08
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 316 -
Rwork0.278 5872 -
obs--95.97 %
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)
10.0509-0.1549-0.0961.35260.79610.66950.05830.00560.0068-0.0564-0.12220.2327-0.03290.06010.06390.134-0.0071-0.02330.1241-0.04920.18977.60937.079-19.454
20.56150.20040.24020.6570.15050.985-0.0108-0.0387-0.0421-0.0848-0.05090.06660.0191-0.01060.06170.027-0.0032-0.00660.1847-0.02470.19538.7064.098-12.345
30.4530.8047-0.58841.7758-1.56621.54830.33740.00720.13050.3847-0.13980.2508-0.120.2271-0.19760.38670.06680.11650.1543-0.0880.117410.69939.0344.063
40.7384-0.2694-0.47730.5503-0.23281.009-0.047-0.2775-0.0194-0.0215-0.02610.02-0.01940.18210.07310.03770.0176-0.01020.3070.00930.154818.8916.6098.24
50.03210.0376-0.18340.2589-0.77532.59090.062-0.020.0124-0.1142-0.05920.01320.12410.1508-0.00270.26820.01850.01350.1285-0.03190.062114.3448.29634.583
60.19580.1289-0.79680.4791-0.70973.3451-0.03380.0026-0.00520.1038-0.0553-0.10090.03250.01540.08910.1986-0.0015-0.05810.1449-0.02380.09827.43678.08165.588
70.31250.24280.37360.363-0.29862.53030.08210.00360.02580.0529-0.05060.06230.10520.1759-0.03150.1990.032-0.01340.1492-0.00110.085515.67746.13358.729
80.04960.0409-0.33261.5601-0.08662.4833-0.0288-0.0169-0.0068-0.197-0.0517-0.1158-0.06670.14370.08050.2294-0.0699-0.03440.12560.02810.114614.78182.95842.519
91.87971.0142-3.08862.0527-1.26745.2048-0.23660.0822-0.0622-0.46480.1389-0.07440.3355-0.17890.09770.1907-0.1208-0.02070.2025-0.01220.05527.66977.02145.42
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 163
2X-RAY DIFFRACTION2B31 - 163
3X-RAY DIFFRACTION3C28 - 163
4X-RAY DIFFRACTION4D31 - 163
5X-RAY DIFFRACTION5E23 - 163
6X-RAY DIFFRACTION6F28 - 163
7X-RAY DIFFRACTION7G28 - 163
8X-RAY DIFFRACTION8H28 - 133
9X-RAY DIFFRACTION9H140 - 163

+
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