[English] 日本語
Yorodumi
- PDB-6bwq: LarC2, the C-terminal domain of a cyclometallase involved in the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bwq
TitleLarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, in complex with MnCTP
ComponentsPyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
KeywordsMETAL BINDING PROTEIN / Lar / nickel transferase / LarC / hexamer / trimer / CTP / nickel / lactate / lactate racemization / lactate racemase
Function / homologypyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase / Nickel insertion protein / Nickel insertion protein / nickel cation binding / protein maturation / lyase activity / CYTIDINE-5'-TRIPHOSPHATE / : / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsFellner, M. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1516126 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.
Authors: Desguin, B. / Fellner, M. / Riant, O. / Hu, J. / Hausinger, R.P. / Hols, P. / Soumillion, P.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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_ncs_dom_lim
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,04113
Polymers33,6382
Non-polymers1,40211
Water2,522140
1
A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
hetero molecules

A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
hetero molecules

A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,12239
Polymers100,9156
Non-polymers4,20733
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area32390 Å2
ΔGint-269 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.215, 97.215, 97.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-502-

MN

21B-506-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 274 through 275 and (name N...
21(chain B and (resid 274 through 357 or (resid 358...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPALAALA(chain A and ((resid 274 through 275 and (name N...AA274 - 2753 - 4
12THRTHRGLNGLN(chain A and ((resid 274 through 275 and (name N...AA272 - 4151 - 144
13THRTHRGLNGLN(chain A and ((resid 274 through 275 and (name N...AA272 - 4151 - 144
14THRTHRGLNGLN(chain A and ((resid 274 through 275 and (name N...AA272 - 4151 - 144
15THRTHRGLNGLN(chain A and ((resid 274 through 275 and (name N...AA272 - 4151 - 144
21ASPASPMETMET(chain B and (resid 274 through 357 or (resid 358...BB274 - 3573 - 86
22GLNGLNGLNGLN(chain B and (resid 274 through 357 or (resid 358...BB35887
23ASPASPGLNGLN(chain B and (resid 274 through 357 or (resid 358...BB274 - 4153 - 144
24ASPASPGLNGLN(chain B and (resid 274 through 357 or (resid 358...BB274 - 4153 - 144
25ASPASPGLNGLN(chain B and (resid 274 through 357 or (resid 358...BB274 - 4153 - 144
26ASPASPGLNGLN(chain B and (resid 274 through 357 or (resid 358...BB274 - 4153 - 144

-
Components

#1: Protein Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein / P2TMN nickel insertion protein / Lactate racemase accessory protein LarC / Lactate racemase ...P2TMN nickel insertion protein / Lactate racemase accessory protein LarC / Lactate racemase activation protein LarC / Lactate racemase maturation protein LarC / Lactate racemization operon protein LarC / Nickel-pincer cofactor biosynthesis protein LarC


Mass: 16819.143 Da / Num. of mol.: 2 / Fragment: LarC2 domain of LarC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Plasmid: pET-22b_pGIR051 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: F9UST1
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.28 Å3/Da / Density % sol: 45.96 % / Mosaicity: 0.16 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.34 ul ~8 mg/ml LarC (100 mM Tris-HCl pH 7.5, 300 mM NaCl) were mixed with 0.17 ul of reservoir solution. Sitting drop reservoir contained 100 ul of 0.1 M MES monohydrate pH 6.5, 12% w/v ...Details: 0.34 ul ~8 mg/ml LarC (100 mM Tris-HCl pH 7.5, 300 mM NaCl) were mixed with 0.17 ul of reservoir solution. Sitting drop reservoir contained 100 ul of 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000. Crystal grew within two months. The crystal was soaked in ~15 mM cytidine triphosphate, ~54 mM manganese chloride + reservoir solution for 28 minutes and then for 2 minutes in 20% Polyethylene glycol 400, 80% reservoir solution.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.35
ReflectionResolution: 1.85→48.61 Å / Num. obs: 26499 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.043 / Rrim(I) all: 0.123 / Net I/σ(I): 11.7 / Num. measured all: 222377
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.898.51.04416230.6150.3761.11199.4
9.06-48.617.20.0472640.9990.0190.05199.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.8 Å48.61 Å
Translation4.8 Å48.61 Å

-
Processing

Software
NameVersionClassification
XDS2.99data reduction
Aimless0.5.32data scaling
PHASER2.8.0phasing
PHENIX1.12-2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BWO

6bwo


Resolution: 1.85→48.608 Å / Cross valid method: THROUGHOUT / σ(F): 2.21 / Phase error: 29.34
RfactorNum. reflection% reflection
Rfree0.1922 3870 7.64 %
Rwork0.1442 --
obs0.1496 25327 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.69 Å2 / Biso mean: 28.1284 Å2 / Biso min: 15.26 Å2
Refinement stepCycle: final / Resolution: 1.85→48.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 67 140 2467
Biso mean--38.78 34.08 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112387
X-RAY DIFFRACTIONf_angle_d0.9863222
X-RAY DIFFRACTIONf_chiral_restr0.056378
X-RAY DIFFRACTIONf_plane_restr0.006404
X-RAY DIFFRACTIONf_dihedral_angle_d9.6011414
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1298X-RAY DIFFRACTION10.86TORSIONAL
12B1298X-RAY DIFFRACTION10.86TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8491-1.8810.27381880.25322311249992
1.881-1.91520.25551890.2442367255692
1.9152-1.9520.2431940.23592359255392
1.952-1.99180.27451960.23462298249492
1.9918-2.03510.24491940.21542387258192
2.0351-2.08240.21071900.22072322251292
2.0824-2.13450.21981920.19982327251992
2.1345-2.19220.23181960.19242339253592
2.1922-2.25660.19592020.17642349255192
2.2566-2.32940.20211850.1692355254092
2.3294-2.41260.24931980.16852335253392
2.4126-2.50910.25241860.16862316250292
2.5091-2.62310.2111880.17052361254993
2.6231-2.76130.191910.15242330252192
2.7613-2.9340.23251980.14322343254192
2.934-3.16010.19441890.13842313250292
3.1601-3.47730.15051970.12732303250091
3.4773-3.97860.18211860.10862330251692
3.9786-5.00540.16732010.09572341254292
5.0054-24.30580.13912000.11062358255892
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)
18.3696-0.03926.85330.5722-1.56449.0905-0.1767-0.13730.22110.0553-0.02250.036-0.22510.13130.22670.22440.00490.0440.1425-0.00380.192839.0323-1.30141.7921
27.1816-0.01426.85550.3383-0.00626.7898-0.0851-0.66450.1330.0906-0.0837-0.0405-0.0225-0.7950.06430.1995-0.00180.02860.24970.00020.208926.33991.58933.0644
30.9907-0.02281.22640.8216-0.33756.79210.0157-0.0964-0.05430.080.01660.07630.172-0.0726-0.03190.14770.01260.03080.18580.00140.219635.4621-2.88870.2504
45.3776.09294.1817.31984.70563.25050.1379-0.0499-0.32230.3591-0.0642-0.26070.18610.1687-0.07650.18780.02740.01980.22950.02040.163947.35041.53368.5734
58.9243-6.84443.35396.3257-1.88225.3269-0.017-0.07040.22340.1137-0.1744-0.0502-0.03880.25910.16820.1764-0.05890.02630.20970.01180.188734.969323.944320.7205
63.6447-5.0495-1.61056.88382.1351.2981-0.0524-0.25180.39430.06450.2671-0.4090.10960.1435-0.22890.2102-0.0113-0.01050.24050.00560.178742.086921.185817.7951
77.6361-5.73871.68794.5492-2.39096.6510.0578-0.04530.0248-0.24180.05940.10710.1073-0.4119-0.10240.1782-0.02950.00670.2064-0.02610.182323.403425.932111.4998
83.4994-0.94215.00273.96730.03037.818-0.21770.31950.54270.0976-0.1066-0.0622-0.12480.69450.40850.2066-0.05180.01860.233-0.0130.258534.906830.350412.6114
96.956-0.8617.03860.830.33798.8307-0.0773-0.1135-0.27010.06570.1354-0.0544-0.1813-0.04630.03370.2162-0.0010.02750.15680.03190.197628.076224.1189-10.1549
107.74910.46088.01351.32270.78558.38370.0587-0.40040.1667-0.0608-0.09360.1270.0105-0.43520.01020.173-0.01550.0050.1962-0.00570.153724.428620.65751.0028
119.61320.57590.56491.0105-0.16740.3146-0.004-0.0596-0.08260.00540.02480.02910.0755-0.0071-0.01650.2012-0.00740.00820.1783-0.01560.133130.893120.5406-9.4754
128.47122.10052.56591.91181.54973.76570.0736-0.07660.37690.1941-0.10090.24080.0258-0.19330.07160.24060.02960.05260.1731-0.00230.246822.272330.1638-6.7193
132.35233.64982.00315.60973.13671.8020.1034-0.02760.0978-0.1516-0.17420.2966-0.1287-0.07050.04630.18430.0088-0.00480.2570.01810.21818.474620.0776-20.1051
146.513-2.40633.48063.06050.31573.2826-0.1775-0.0727-0.05660.56070.30420.4472-0.6413-0.5896-0.17390.2388-0.00530.04160.2633-0.07010.18896.3598-2.0026-7.4867
153.32270.5316-0.05037.5512-5.74454.4387-0.10010.18340.22030.28610.05330.2998-0.5538-0.3547-0.13410.19540.0170.00010.2471-0.03030.24838.22020.405-11.3212
164.0464-4.21684.05497.4794-5.34484.4507-0.49590.5342-0.433-0.4356-0.19670.33151.0662-0.26430.43550.2109-0.0970.03590.4946-0.08770.309710.9345-0.4253-17.1253
176.5459-3.26433.34794.4425-5.67127.58130.0819-0.24260.21530.1262-0.0991-0.24070.0276-0.01530.02870.2317-0.03580.00070.2834-0.00780.195215.3312-3.40594.363
187.7885-0.83735.62398.4057-0.42564.16890.05220.9042-0.0845-0.36180.0291-0.00250.30940.6964-0.14660.23710.03250.04850.3179-0.00630.17213.9315-9.2445-6.1055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 272 through 287 )A272 - 287
2X-RAY DIFFRACTION2chain 'A' and (resid 288 through 300 )A288 - 300
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 347 )A301 - 347
4X-RAY DIFFRACTION4chain 'A' and (resid 348 through 357 )A348 - 357
5X-RAY DIFFRACTION5chain 'A' and (resid 358 through 368 )A358 - 368
6X-RAY DIFFRACTION6chain 'A' and (resid 369 through 387 )A369 - 387
7X-RAY DIFFRACTION7chain 'A' and (resid 388 through 401 )A388 - 401
8X-RAY DIFFRACTION8chain 'A' and (resid 402 through 415 )A402 - 415
9X-RAY DIFFRACTION9chain 'B' and (resid 274 through 287 )B274 - 287
10X-RAY DIFFRACTION10chain 'B' and (resid 288 through 300 )B288 - 300
11X-RAY DIFFRACTION11chain 'B' and (resid 301 through 327 )B301 - 327
12X-RAY DIFFRACTION12chain 'B' and (resid 328 through 347 )B328 - 347
13X-RAY DIFFRACTION13chain 'B' and (resid 348 through 357 )B348 - 357
14X-RAY DIFFRACTION14chain 'B' and (resid 358 through 368 )B358 - 368
15X-RAY DIFFRACTION15chain 'B' and (resid 369 through 378 )B369 - 378
16X-RAY DIFFRACTION16chain 'B' and (resid 379 through 387 )B379 - 387
17X-RAY DIFFRACTION17chain 'B' and (resid 388 through 401 )B388 - 401
18X-RAY DIFFRACTION18chain 'B' and (resid 402 through 415 )B402 - 415

+
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