[English] 日本語
Yorodumi
- PDB-2gu2: Crystal Structure of an Aspartoacylase from Rattus norvegicus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gu2
TitleCrystal Structure of an Aspartoacylase from Rattus norvegicus
ComponentsAspa protein
KeywordsHYDROLASE / Aspartoacylase family / Aminoacylase-2 / ACY-2 / ACY2_RAT / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Aspartate and asparagine metabolism / aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding ...Aspartate and asparagine metabolism / aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
N-terminal domain of TfIIb - #160 / Aspartoacylase / Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / N-terminal domain of TfIIb / Zn peptidases / Single Sheet / Aminopeptidase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.805 Å
AuthorsBitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of aspartoacylase, the brain enzyme impaired in Canavan disease.
Authors: Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / McCoy, J.G. / Phillips, G.N.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 21, 2022Group: 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_conn.ptnr2_label_seq_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: Aspa protein
B: Aspa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5569
Polymers70,9452
Non-polymers6117
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-155 kcal/mol
Surface area25220 Å2
MethodPISA
2
A: Aspa protein
B: Aspa protein
hetero molecules

A: Aspa protein
B: Aspa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,11218
Polymers141,8904
Non-polymers1,22214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8950 Å2
ΔGint-327 kcal/mol
Surface area48660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.581, 135.778, 54.033
Angle α, β, γ (deg.)90.00, 101.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-744-

HOH

21A-755-

HOH

31B-776-

HOH

DetailsThe biological unit is likely a dimer with one biological unit in the asymmetric unit (chains A & B)

-
Components

#1: Protein Aspa protein


Mass: 35472.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: BC078813, UNIPROT-Q9R1T5 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q9R1T5, aspartoacylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 MES PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (1.9 M Ammonium sulfate, 0.10 ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 MES PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (1.9 M Ammonium sulfate, 0.10 M HEPPS PH 8.5). Crystal cryo-protected with well solution supplemented with a final concentration of 30% Ethylene glycol, temperature 293K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97928, 0.95373
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 19, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979281
20.953731
ReflectionResolution: 1.8→80 Å / Num. obs: 58208 / % possible obs: 97.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.093 / Χ2: 1.097 / Net I/σ(I): 9.949
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.8-1.844.20.472.16734240.76686.6
1.84-1.894.90.4437010.78493.9
1.89-1.945.90.3838850.82497
1.94-26.70.34239100.85697.7
2-2.067.30.29338650.94997.9
2.06-2.137.60.2338820.97698.1
2.13-2.227.60.19139111.08398.3
2.22-2.327.60.16739081.16898.5
2.32-2.447.60.14239381.20598.7
2.44-2.67.60.12439091.22298.8
2.6-2.87.60.10239401.27198.9
2.8-3.087.70.08739441.29599.2
3.08-3.527.60.0739641.26299.3
3.52-4.447.60.05740011.13399.6
4.44-807.50.0640261.20899.7

-
Phasing

PhasingMethod: MAD
Phasing MAD set

Highest resolution: 2.4 Å / Lowest resolution: 40.5 Å

IDR cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_1000024757617
ISO_20.6350.7021.9851.48224741617
ANO_10.61601.8990247340
ANO_20.79300.760247340
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_110.39-40.5000028636
ISO_17.47-10.39000050933
ISO_16.14-7.47000065828
ISO_15.33-6.14000078533
ISO_14.77-5.33000089035
ISO_14.36-4.77000097828
ISO_14.04-4.360000104932
ISO_13.78-4.040000114530
ISO_13.57-3.780000119129
ISO_13.39-3.570000128829
ISO_13.23-3.390000135334
ISO_13.09-3.230000140830
ISO_12.97-3.090000145433
ISO_12.87-2.970000153526
ISO_12.77-2.870000159628
ISO_12.68-2.770000162733
ISO_12.6-2.680000166627
ISO_12.53-2.60000173032
ISO_12.46-2.530000176625
ISO_12.4-2.460000184336
ANO_110.39-40.50.51102.11502840
ANO_17.47-10.390.55102.14305070
ANO_16.14-7.470.53202.38806580
ANO_15.33-6.140.54602.25307840
ANO_14.77-5.330.59702.06308870
ANO_14.36-4.770.64901.83609780
ANO_14.04-4.360.61601.925010490
ANO_13.78-4.040.62101.981011450
ANO_13.57-3.780.64801.909011900
ANO_13.39-3.570.60602.01012870
ANO_13.23-3.390.59602.092013520
ANO_13.09-3.230.60802.018014080
ANO_12.97-3.090.58401.996014540
ANO_12.87-2.970.60301.959015320
ANO_12.77-2.870.61401.848015950
ANO_12.68-2.770.61301.818016260
ANO_12.6-2.680.65901.642016660
ANO_12.53-2.60.68301.56017290
ANO_12.46-2.530.70401.413017630
ANO_12.4-2.460.73301.304018400
ISO_210.39-40.50.5240.7032.4591.49928636
ISO_27.47-10.390.5610.7592.3971.71250933
ISO_26.14-7.470.540.5362.6232.04165828
ISO_25.33-6.140.5850.6412.5161.98278533
ISO_24.77-5.330.6240.6442.2171.82689035
ISO_24.36-4.770.6650.6522.011.61597828
ISO_24.04-4.360.6460.5651.9681.655104932
ISO_23.78-4.040.6280.681.9321.642114530
ISO_23.57-3.780.6360.8141.941.29119129
ISO_23.39-3.570.6190.71.9691.329128829
ISO_23.23-3.390.6261.0581.9791.269135334
ISO_23.09-3.230.6450.6491.9851.481140830
ISO_22.97-3.090.6530.8061.9741.064145433
ISO_22.87-2.970.6440.7961.9781.234153526
ISO_22.77-2.870.6480.7171.8920.946159628
ISO_22.68-2.770.6720.7991.8541.303162733
ISO_22.6-2.680.6650.7441.7661.109166627
ISO_22.53-2.60.6660.5941.6581.324173032
ISO_22.46-2.530.681.0361.5371.065176625
ISO_22.4-2.460.7050.7941.4560.927182736
ANO_210.39-40.50.68800.8702850
ANO_27.47-10.390.7100.89805070
ANO_26.14-7.470.67101.09606580
ANO_25.33-6.140.70200.97407840
ANO_24.77-5.330.71800.94608890
ANO_24.36-4.770.75500.84909780
ANO_24.04-4.360.75400.866010490
ANO_23.78-4.040.7700.866011450
ANO_23.57-3.780.78300.859011910
ANO_23.39-3.570.75600.862012880
ANO_23.23-3.390.77500.828013530
ANO_23.09-3.230.78900.806014080
ANO_22.97-3.090.79200.744014540
ANO_22.87-2.970.80800.733015350
ANO_22.77-2.870.82400.671015950
ANO_22.68-2.770.83700.632016270
ANO_22.6-2.680.86200.607016650
ANO_22.53-2.60.88300.559017300
ANO_22.46-2.530.89800.489017660
ANO_22.4-2.460.91100.462018270
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
112.205-5.83824.003SE17.541.02
231.29130.9250.296SE21.320.95
36.617-2.08224.053SE20.10.98
410.1647.07419.77SE16.370.89
528.0844.0483.554SE190.84
62.484-1.23120.616SE40.611.11
730.06639.38717.015SE29.180.91
838.61739.973.465SE21.30.83
946.346-30.5342.189SE29.580.96
1076.85-1.49417.262SE29.960.68
Phasing dmFOM : 0.57 / FOM acentric: 0.57 / FOM centric: 0.61 / Reflection: 58207 / Reflection acentric: 57196 / Reflection centric: 1011
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.2-41.7520.960.960.9426032465138
3.2-5.20.940.950.8679557744211
2.6-3.20.850.850.7699029721181
2.3-2.60.650.650.5599819821160
1.9-2.30.380.380.311763117404227
1.8-1.90.150.150.15101351004194

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RESOLVE2.06phasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
SHELXEmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.805→41.75 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.15 / SU B: 4.361 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2955 5.077 %Random
Rwork0.1494 ---
all0.152 ---
obs-58208 97.248 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.168 Å20 Å20.118 Å2
2--0.098 Å20 Å2
3----0.219 Å2
Refinement stepCycle: LAST / Resolution: 1.805→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 27 552 5441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225081
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.976910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80624.335233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56115876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5251527
X-RAY DIFFRACTIONr_chiral_restr0.1240.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023871
X-RAY DIFFRACTIONr_nbd_refined0.2080.22473
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23498
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2423
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.237
X-RAY DIFFRACTIONr_mcbond_it1.86823216
X-RAY DIFFRACTIONr_mcangle_it2.99245071
X-RAY DIFFRACTIONr_scbond_it5.09862110
X-RAY DIFFRACTIONr_scangle_it7.02481831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.805-1.8520.2681930.20835230.211441484.187
1.852-1.9030.251950.18738570.19429794.298
1.903-1.9580.2151880.15938820.162418697.229
1.958-2.0180.2222020.14837660.152406197.71
2.018-2.0840.1721920.14236750.143394498.048
2.084-2.1570.1811760.13735910.139384198.073
2.157-2.2390.1681950.13833960.14365298.33
2.239-2.330.21920.14132860.145353198.499
2.33-2.4340.2051570.14531920.147339598.645
2.434-2.5520.211510.15530640.158325598.771
2.552-2.690.2061780.14928710.153308398.897
2.69-2.8530.21550.1527600.153294499.015
2.853-3.050.1851330.15525980.157275399.201
3.05-3.2940.2141310.14724090.15256099.219
3.294-3.6070.1661280.13922210.141236199.492
3.607-4.0320.1941080.13220160.134213499.531
4.032-4.6530.154970.13117930.132189699.684
4.653-5.6940.165780.14914990.15158199.747
5.694-8.0290.229660.1911890.192125799.841
8.029-75.3780.229400.1866650.18871099.296
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.886-0.0988-0.20490.84350.33750.6662-0.04390.0717-0.0577-0.15190.082-0.0151-0.1135-0.0156-0.0381-0.021-0.03480.0098-0.029-0.0263-0.043921.13441.232-1.392
21.4881-0.43310.26840.23230.21560.8607-0.0170.0488-0.1797-0.02280.02030.0458-0.0147-0.1688-0.0033-0.0525-0.0230.0022-0.0197-0.00680.01136.62933.8342.071
30.2746-0.01280.02240.57640.33680.6623-0.0348-0.0014-0.0990.02780.0315-0.04850.01330.05310.0032-0.0627-0.00970.0145-0.0411-0.02070.00429.2335.37513.316
40.6440.26910.00181.43110.83440.7766-0.010.01890.02580.1478-0.09470.24690.0438-0.15420.1047-0.01580.00770.0207-0.0336-0.0196-0.031714.9465.14430.743
50.94730.3292-0.88663.92681.93493.37030.01730.16720.1069-0.2799-0.3210.8938-0.4172-0.7820.3036-0.06640.1285-0.10430.105-0.06720.18053.05573.05122.113
60.29990.1287-0.14550.77730.48370.6607-0.04620.04680.0533-0.04080.04560.0236-0.0957-0.010.0005-0.013-0.0008-0.0236-0.04820.0029-0.049128.50770.57320.465
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 704 - 70
22AA71 - 10571 - 105
33AA106 - 310106 - 310
44BB4 - 704 - 70
55BB71 - 10571 - 105
66BB106 - 310106 - 310

+
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