[English] 日本語
Yorodumi
- PDB-8ryi: Metformin hydrolase from Aminobacter niigataensis MD1 with urea i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ryi
TitleMetformin hydrolase from Aminobacter niigataensis MD1 with urea in the active site
Components
  • Agmatinase family protein
  • Arginase family protein
KeywordsMETAL BINDING PROTEIN / Metformin hydrolase / ureohydrolase / nickel-dependent
Function / homologydicarbonimidic diamide / NICKEL (II) ION / UREA / : / :
Function and homology information
Biological speciesAminobacter niigataensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsFleming, J.R. / Lutz, H. / Bachmann, A. / Mayans, O.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)681777European Union
CitationJournal: Nat Commun / Year: 2024
Title: Metformin hydrolase is a recently evolved nickel-dependent heteromeric ureohydrolase.
Authors: Sinn, M. / Riede, L. / Fleming, J.R. / Funck, D. / Lutz, H. / Bachmann, A. / Mayans, O. / Hartig, J.S.
History
DepositionFeb 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Arginase family protein
B: Agmatinase family protein
A: Arginase family protein
E: Agmatinase family protein
F: Arginase family protein
D: Arginase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,97915
Polymers236,3786
Non-polymers6019
Water16,718928
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.990, 86.520, 168.410
Angle α, β, γ (deg.)90.000, 113.990, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11E-560-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 15 or resid 28...
d_2ens_1(chain "C" and (resid 7 through 15 or resid 28...
d_3ens_1(chain "D" and (resid 7 through 15 or resid 28...
d_4ens_1(chain "F" and (resid 7 through 15 or resid 28...
d_1ens_2(chain "B" and (resid 8 through 11 or resid 13...
d_2ens_2(chain "E" and (resid 8 through 11 or resid 13...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1TYRTYRGLYGLYAC7 - 157 - 15
d_12ens_1ILEILELEULEUAC28 - 3128 - 31
d_13ens_1SERSERALAALAAC33 - 4833 - 48
d_14ens_1TYRTYRPROPROAC50 - 7150 - 71
d_15ens_1GLUGLUGLYGLYAC73 - 10073 - 100
d_16ens_1SERSERPROPROAC108 - 109108 - 109
d_17ens_1VALVALHISHISAC111 - 113111 - 113
d_18ens_1ARGARGTYRTYRAC115 - 117115 - 117
d_19ens_1ALAALAGLUGLUAC119 - 175119 - 175
d_110ens_1ASNASNILEILEAC177 - 194177 - 194
d_111ens_1ASNASNMETMETAC196 - 225196 - 225
d_112ens_1ASPASPLEULEUAC227 - 276227 - 276
d_113ens_1SERSERMETMETAC278 - 281278 - 281
d_114ens_1ARGARGALAALAAC283 - 289283 - 289
d_115ens_1ARGARGALAALAAC291 - 317291 - 317
d_116ens_1VALVALASPASPAC319 - 336319 - 336
d_117ens_1LYSLYSARGARGAC338 - 341338 - 341
d_21ens_1TYRTYRGLYGLYCA7 - 157 - 15
d_22ens_1ILEILELEULEUCA28 - 3128 - 31
d_23ens_1SERSERALAALACA33 - 4833 - 48
d_24ens_1TYRTYRPROPROCA50 - 7150 - 71
d_25ens_1GLUGLUGLYGLYCA73 - 10073 - 100
d_26ens_1SERSERPROPROCA108 - 109108 - 109
d_27ens_1VALVALHISHISCA111 - 113111 - 113
d_28ens_1ARGARGTYRTYRCA115 - 117115 - 117
d_29ens_1ALAALAGLUGLUCA119 - 175119 - 175
d_210ens_1ASNASNILEILECA177 - 194177 - 194
d_211ens_1ASNASNMETMETCA196 - 225196 - 225
d_212ens_1ASPASPLEULEUCA227 - 276227 - 276
d_213ens_1SERSERMETMETCA278 - 281278 - 281
d_214ens_1ARGARGALAALACA283 - 289283 - 289
d_215ens_1ARGARGALAALACA291 - 317291 - 317
d_216ens_1VALVALASPASPCA319 - 336319 - 336
d_217ens_1LYSLYSARGARGCA338 - 341338 - 341
d_31ens_1TYRTYRGLYGLYDF7 - 157 - 15
d_32ens_1ILEILELEULEUDF28 - 3128 - 31
d_33ens_1SERSERALAALADF33 - 4833 - 48
d_34ens_1TYRTYRPROPRODF50 - 7150 - 71
d_35ens_1GLUGLUGLYGLYDF73 - 10073 - 100
d_36ens_1SERSERPROPRODF108 - 109108 - 109
d_37ens_1VALVALHISHISDF111 - 113111 - 113
d_38ens_1ARGARGTYRTYRDF115 - 117115 - 117
d_39ens_1ALAALAGLUGLUDF119 - 175119 - 175
d_310ens_1ASNASNILEILEDF177 - 194177 - 194
d_311ens_1ASNASNMETMETDF196 - 225196 - 225
d_312ens_1ASPASPLEULEUDF227 - 276227 - 276
d_313ens_1SERSERMETMETDF278 - 281278 - 281
d_314ens_1ARGARGALAALADF283 - 289283 - 289
d_315ens_1ARGARGALAALADF291 - 317291 - 317
d_316ens_1VALVALASPASPDF319 - 336319 - 336
d_317ens_1LYSLYSARGARGDF338 - 341338 - 341
d_41ens_1TYRTYRGLYGLYFE7 - 157 - 15
d_42ens_1ILEILELEULEUFE28 - 3128 - 31
d_43ens_1SERSERALAALAFE33 - 4833 - 48
d_44ens_1TYRTYRPROPROFE50 - 7150 - 71
d_45ens_1GLUGLUGLYGLYFE73 - 10073 - 100
d_46ens_1SERSERPROPROFE108 - 109108 - 109
d_47ens_1VALVALHISHISFE111 - 113111 - 113
d_48ens_1ARGARGTYRTYRFE115 - 117115 - 117
d_49ens_1ALAALAGLUGLUFE119 - 175119 - 175
d_410ens_1ASNASNILEILEFE177 - 194177 - 194
d_411ens_1ASNASNMETMETFE196 - 225196 - 225
d_412ens_1ASPASPLEULEUFE227 - 276227 - 276
d_413ens_1SERSERMETMETFE278 - 281278 - 281
d_414ens_1ARGARGALAALAFE283 - 289283 - 289
d_415ens_1ARGARGALAALAFE291 - 317291 - 317
d_416ens_1VALVALASPASPFE319 - 336319 - 336
d_417ens_1LYSLYSARGARGFE338 - 341338 - 341
d_11ens_2THRTHRTRPTRPBB8 - 1127 - 30
d_12ens_2PHEPHEHISHISBB13 - 1832 - 37
d_13ens_2GLYGLYGLYGLYBB20 - 2639 - 45
d_14ens_2ASNASNSERSERBB28 - 4347 - 62
d_15ens_2GLYGLYILEILEBB45 - 6264 - 81
d_16ens_2GLUGLUVALVALBB64 - 8283 - 101
d_17ens_2ALAALAARGARGBB84 - 94103 - 113
d_18ens_2ALAALAGLNGLNBB96 - 134115 - 153
d_19ens_2TYRTYRALAALABB136 - 165155 - 184
d_110ens_2ALAALAILEILEBB167 - 249186 - 268
d_111ens_2ARGARGALAALABB251 - 287270 - 306
d_112ens_2ALAALAGLYGLYBB290 - 309309 - 328
d_113ens_2HISHISARGARGBB311 - 351330 - 370
d_114ens_2GLNGLNPROPROBB353 - 357372 - 376
d_115ens_2C5JC5JC5JC5JBG401
d_116ens_2UREUREUREUREBH402
d_117ens_2NINININIBI403
d_21ens_2THRTHRTRPTRPED8 - 1127 - 30
d_22ens_2PHEPHEHISHISED13 - 1832 - 37
d_23ens_2GLYGLYGLYGLYED20 - 2639 - 45
d_24ens_2ASNASNSERSERED28 - 4347 - 62
d_25ens_2GLYGLYILEILEED45 - 6264 - 81
d_26ens_2GLUGLUVALVALED64 - 8283 - 101
d_27ens_2ALAALAARGARGED84 - 94103 - 113
d_28ens_2ALAALAGLNGLNED96 - 134115 - 153
d_29ens_2TYRTYRALAALAED136 - 165155 - 184
d_210ens_2ALAALAILEILEED167 - 249186 - 268
d_211ens_2ARGARGALAALAED251 - 287270 - 306
d_212ens_2ALAALAGLYGLYED290 - 309309 - 328
d_213ens_2HISHISARGARGED311 - 351330 - 370
d_214ens_2GLNGLNPROPROED353 - 357372 - 376
d_215ens_2C5JC5JC5JC5JEK401
d_216ens_2UREUREUREUREEL402
d_217ens_2NINININIEM403

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.805097868285, 0.214607599039, -0.552956599489), (0.223411809868, -0.753872714633, -0.617869802907), (-0.549458447651, -0.620982695868, 0.558995443396)68.8313433438, -18.1403293273, 16.9389608853
2given(0.880424658424, -0.193918064278, 0.432721856607), (0.285299055453, -0.512279373046, -0.810045858522), (0.378757006267, 0.836639485261, -0.395698751458)-17.7252558294, -9.9541962071, 60.0336638414
3given(-0.858781374967, -0.405283187845, -0.313432748224), (-0.266493091598, -0.169142466392, 0.948879475062), (-0.437579686616, 0.898407682354, 0.0372512301514)48.4212046343, -50.8257274565, 66.4932146403
4given(-0.80318125102, 0.220856451903, -0.553283205658), (0.219213266632, -0.75400955705, -0.619205241911), (-0.553936297549, -0.618621059721, 0.557191675034)68.8296704902, -18.0207791132, 17.2970892246

-
Components

-
Protein , 2 types, 6 molecules CAFDBE

#1: Protein
Arginase family protein


Mass: 38024.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aminobacter niigataensis (bacteria) / Strain: MD1 / Gene: N7E70_023835 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9E9PPA5
#2: Protein Agmatinase family protein


Mass: 42140.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aminobacter niigataensis (bacteria) / Strain: MD1 / Gene: N7E70_023840 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9E9PQ69

-
Non-polymers , 5 types, 937 molecules

#3: Chemical ChemComp-C5J / dicarbonimidic diamide


Mass: 103.080 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5N3O2
#4: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 20 % (w/v) PEG 3350, 100 mM Bis Tris Propane HCl pH 6.5, 200mM NaF

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.06→29.97 Å / Num. obs: 130397 / % possible obs: 97.9 % / Redundancy: 7.18 % / Biso Wilson estimate: 45.57 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.31
Reflection shellResolution: 2.06→2.08 Å / Redundancy: 7.47 % / Num. unique obs: 3627 / CC1/2: 0.357 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→29.97 Å / SU ML: 0.2669 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1989 6573 5.04 %
Rwork0.1685 123796 -
obs0.1701 130369 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.53 Å2
Refinement stepCycle: LAST / Resolution: 2.06→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15674 0 27 928 16629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007616246
X-RAY DIFFRACTIONf_angle_d0.924822019
X-RAY DIFFRACTIONf_chiral_restr0.05772359
X-RAY DIFFRACTIONf_plane_restr0.00772926
X-RAY DIFFRACTIONf_dihedral_angle_d12.90746042
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS0.465827553805
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS0.633874305975
ens_1d_4CAX-RAY DIFFRACTIONTorsion NCS0.726242887527
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.285642869815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.080.38292150.36984020X-RAY DIFFRACTION97.99
2.08-2.110.3122300.33424168X-RAY DIFFRACTION98.15
2.11-2.130.34292130.29974067X-RAY DIFFRACTION98.14
2.13-2.160.30041970.27334184X-RAY DIFFRACTION98.38
2.16-2.190.28312310.25534046X-RAY DIFFRACTION98.5
2.19-2.220.2982360.25084137X-RAY DIFFRACTION98.4
2.22-2.250.26932240.24114122X-RAY DIFFRACTION98.75
2.25-2.280.2482220.23994126X-RAY DIFFRACTION98.5
2.28-2.320.27472260.23024168X-RAY DIFFRACTION98.74
2.32-2.360.26012230.23454094X-RAY DIFFRACTION98.61
2.36-2.40.25082160.22164153X-RAY DIFFRACTION98.78
2.4-2.440.27752280.21414131X-RAY DIFFRACTION98.49
2.44-2.490.24352210.20794138X-RAY DIFFRACTION98.66
2.49-2.540.24092050.19584149X-RAY DIFFRACTION98.84
2.54-2.60.23162200.19024151X-RAY DIFFRACTION98.53
2.6-2.660.24632220.19164153X-RAY DIFFRACTION98.51
2.66-2.720.23672090.18454137X-RAY DIFFRACTION98.37
2.72-2.80.21652250.18894095X-RAY DIFFRACTION97.63
2.8-2.880.25172050.19343793X-RAY DIFFRACTION89.96
2.88-2.970.21732170.18613985X-RAY DIFFRACTION95.05
2.97-3.080.21232170.174164X-RAY DIFFRACTION99.32
3.08-3.20.19492320.16674207X-RAY DIFFRACTION99.35
3.2-3.340.21292090.17384186X-RAY DIFFRACTION99.39
3.34-3.520.19012010.15944192X-RAY DIFFRACTION99.5
3.52-3.740.16762280.14524229X-RAY DIFFRACTION99.31
3.74-4.030.16512310.13914199X-RAY DIFFRACTION99.33
4.03-4.430.14242410.12394147X-RAY DIFFRACTION98.85
4.43-5.070.15922240.12554157X-RAY DIFFRACTION98.01
5.07-6.380.19041930.15473943X-RAY DIFFRACTION92.16
6.38-29.970.16952120.14994355X-RAY DIFFRACTION99.05
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)
11.5611355684-0.1508380178940.06879125591062.13847311374-0.4044629047361.05436592345-0.022027881457-0.462830691417-0.7969344664930.2262507546220.2384321252160.7129986533710.206087119463-0.2449438273-0.1173072729640.434441090958-0.02601634398980.02917190565770.5085293730490.315656763260.9796329385519.41504162004-39.738535103623.4736257403
20.889295057683-0.493445125790.06590973947531.577079568950.07710800896820.725571297263-0.0131829236333-0.04312357141550.06287576688890.09290085273620.0723671358658-0.2216457764660.07122468405880.206979742239-0.05309589903530.3184123251130.01523553833-0.01695975375650.392969956808-0.05189869249620.36484781219947.9731400891-22.343989833420.1665112852
31.06596181163-0.37180250102-0.1808988584721.29023571820.06845025094032.11924626879-0.1444100803-0.409293253550.2934272823130.5101616251230.161805320433-0.143967430139-0.2192678346030.16025538743-0.00981416518810.5826660782330.0674435322605-0.09855872610790.491595244925-0.1779958328420.41952868282940.1366939692-0.24125001315649.4571935302
41.147382978-0.3920918897930.1823208289231.51478259885-0.1958836006940.949974733042-0.0324324779135-0.1657848259520.04241424278050.0948249477740.1306606064080.320189149176-0.192875435952-0.219351253293-0.07738461208190.3198093465440.01776690251830.01737781532650.3473040647840.05183573492740.41993189077315.0317131873-2.7171335138915.3371326595
51.22368590055-0.2126222725930.04166167809051.476056826450.2778230473231.40489700614-0.336964648066-0.964646711898-0.3153427592541.16615523710.3916360441680.7592857986640.0940426901446-0.296318962047-0.00432603356151.074786631450.3194993087710.4841136087961.280183733570.3431653795640.878400449204-1.65709930235-14.08557930850.1300182155
61.069241131080.1173487896810.1326840946733.087804758210.1140907989811.467912879510.0151498896299-0.243094432835-0.08504768739190.3558310027280.02912374582690.2137940779290.0104279334045-0.069736136228-0.04865695152050.5362885683270.113081383861-0.06868911223470.479206648174-0.004806807172060.32280267819738.9859321406-38.69462597855.0176869044
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'C' and resid 6 through 341)CC6 - 3411 - 336
22(chain 'B' and resid 8 through 402)BD - F8 - 4021
33(chain 'A' and resid 6 through 342)AI6 - 3421 - 326
44(chain 'E' and resid -3 through 402)EJ - L-3 - 4021
55(chain 'F' and resid 6 through 345)FO6 - 3451 - 324
66(chain 'D' and resid 6 through 345)DP6 - 3451 - 332

+
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