[English] 日本語
Yorodumi
- PDB-6g60: Choline sulfatase from Ensifer (Sinorhizobium) meliloti cocrystal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g60
TitleCholine sulfatase from Ensifer (Sinorhizobium) meliloti cocrystalized with choline
ComponentsCholine-sulfatase
KeywordsHYDROLASE / Choline-sulfatase
Function / homology
Function and homology information


choline biosynthetic process / choline-sulfatase / choline-sulfatase activity / metal ion binding
Similarity search - Function
Choline-sulfatase / Choline sulfatase enzyme C-terminal domain / Choline sulfatase enzyme C terminal / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
CHOLINE ION / Choline-sulfatase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsMartinez-Rodriguez, S. / Camara-Artigas, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding.
Authors: Gavira, J.A. / Camara-Artigas, A. / Neira, J.L. / Torres de Pinedo, J.M. / Sanchez, P. / Ortega, E. / Martinez-Rodriguez, S.
History
DepositionMar 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Mar 8, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_conn_type
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Choline-sulfatase
B: Choline-sulfatase
C: Choline-sulfatase
D: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,77919
Polymers232,5924
Non-polymers1,18615
Water21,9421218
1
A: Choline-sulfatase
C: Choline-sulfatase
hetero molecules

A: Choline-sulfatase
C: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,68318
Polymers232,5924
Non-polymers1,09014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area20110 Å2
ΔGint-95 kcal/mol
Surface area64070 Å2
MethodPISA
2
A: Choline-sulfatase
C: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8419
Polymers116,2962
Non-polymers5457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-52 kcal/mol
Surface area38150 Å2
MethodPISA
3
B: Choline-sulfatase
D: Choline-sulfatase
hetero molecules

B: Choline-sulfatase
D: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,87520
Polymers232,5924
Non-polymers1,28216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area19130 Å2
ΔGint-106 kcal/mol
Surface area64100 Å2
MethodPISA
4
B: Choline-sulfatase
D: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,93710
Polymers116,2962
Non-polymers6418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-54 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.538, 206.898, 116.602
Angle α, β, γ (deg.)90.000, 110.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-605-

SO4

-
Components

#1: Protein
Choline-sulfatase /


Mass: 58148.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: betC, R00949, SMc00127 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69787, choline-sulfatase
#2: Chemical
ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H14NO
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1218 / 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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0 M Lithium sulfate, 0.1M Hepes pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.84→103.45 Å / Num. obs: 411516 / % possible obs: 95.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 27.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.031 / Rrim(I) all: 0.051 / Net I/σ(I): 13.1 / Num. measured all: 563519 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.872.40.50127428114490.6970.40.645294.1
10.08-103.452.50.023367914530.9980.0170.02835.195.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→75.183 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 20514 4.98 %
Rwork0.1688 391002 -
obs0.1703 411516 84.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.68 Å2 / Biso mean: 34.0352 Å2 / Biso min: 13.54 Å2
Refinement stepCycle: final / Resolution: 1.84→75.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16000 0 67 1218 17285
Biso mean--51.37 37.55 -
Num. residues----2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116528
X-RAY DIFFRACTIONf_angle_d1.01822553
X-RAY DIFFRACTIONf_chiral_restr0.0592385
X-RAY DIFFRACTIONf_plane_restr0.0072970
X-RAY DIFFRACTIONf_dihedral_angle_d5.04411681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.86090.34347410.2922128361357784
1.8609-1.88280.31296940.2733123551304979
1.8828-1.90580.29176150.2575121871280278
1.9058-1.92990.28847040.243124921319681
1.9299-1.95530.28316480.2343120951274379
1.9553-1.98210.2686590.2195128601351983
1.9821-2.01040.24357980.2113139381473690
2.0104-2.04040.21726970.1982139071460490
2.0404-2.07230.24947610.1945138351459690
2.0723-2.10630.22447080.1983139521466090
2.1063-2.14260.23567580.1993137631452189
2.1426-2.18160.23027010.1902137871448889
2.1816-2.22350.23366320.1882137701440289
2.2235-2.26890.216320.178137191435188
2.2689-2.31830.22656860.1753135121419887
2.3183-2.37220.21326980.1754134851418386
2.3722-2.43150.20956770.1672133141399185
2.4315-2.49730.19216960.1671130121370884
2.4973-2.57070.18516060.1625126721327882
2.5707-2.65370.19776410.1741118601250177
2.6537-2.74860.22656040.1806118821248677
2.7486-2.85860.21776270.1764118401246776
2.8586-2.98870.21596940.1807135381423287
2.9887-3.14630.21237480.1765133041405286
3.1463-3.34340.18977170.1698131801389785
3.3434-3.60160.16696580.1534129901364884
3.6016-3.9640.15877330.1344128061353983
3.964-4.53750.15845970.1271125141311180
4.5375-5.71650.1626370.141114981213574
5.7165-75.24560.17647470.1596140991484691
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)
10.3627-0.1073-0.05040.0629-0.04340.3682-0.1398-0.07430.04610.10240.10620.07860.0785-0.1143-0.00060.28130.0355-0.02610.21960.00070.178322.68742.690960.3153
20.0195-0.0437-0.04910.09930.06730.0439-0.0580.09060.0956-0.15190.0485-0.0778-0.0239-0.082-0.00180.3103-0.0254-0.07990.28340.0060.189320.7297.799739.6863
30.3829-0.26870.13960.2764-0.08360.1083-0.1483-0.030.01380.01760.110.0102-0.0264-0.0054-0.01020.26370.0308-0.0240.1885-0.01050.136135.7455-2.035657.1804
40.12030.07960.02030.0760.07010.1133-0.10180.2141-0.1523-0.1570.00810.16380.1227-0.124-0.00020.3758-0.0752-0.05810.3446-0.05640.271611.7142-6.729936.3313
50.2641-0.2737-0.04720.2798-0.06240.1347-0.1333-0.0013-0.07880.08680.06710.08820.1618-0.0641-0.00660.2826-0.0029-0.01090.1976-0.00760.150525.5367-7.92552.4666
60.218-0.1717-0.09820.22620.21690.2308-0.1859-0.0764-0.05010.15520.10230.20770.183-0.1694-0.010.3054-0.02380.03890.29550.0320.23827.8792-2.55660.5776
70.27330.088-0.00950.47180.39790.4175-0.1233-0.00590.1280.0326-0.00440.081-0.0354-0.1321-0.03440.16680.0458-0.01110.28620.0050.210210.826514.048251.598
80.0302-0.0224-0.00620.0043-0.0086-0.002-0.0731-0.25380.0940.36060.1125-0.0539-0.01190.0579-00.45350.0383-0.05630.3495-0.03540.267654.79556.193170.8315
90.4627-0.1473-0.24490.25160.09380.783-0.0116-0.0780.0341-0.02050.105-0.02190.04560.12610.07150.16710.02580.01450.2093-0.03060.159537.9842-36.673492.1749
10-0.0433-0.1102-0.11660.08290.13240.0303-0.0357-0.1331-0.21480.18760.16530.22920.3159-0.32010.01240.2766-0.0657-0.05380.26510.0340.289420.1405-42.072581.7998
110.20440.0031-0.09270.33890.09470.41930.0643-0.14320.0431-0.02520.06270.01250.0345-0.03030.04440.15490.0320.0150.2573-0.02320.144228.744-31.5837102.1277
120.0843-0.03210.08380.0834-0.06590.1460.13380.06090.035-0.12360.0919-0.0183-0.2077-0.3090.00870.21650.02780.02060.32060.07380.229620.7644-27.912371.892
130.23890.0006-0.39750.07240.18550.60930.0821-0.04120.1230.00120.0632-0.0314-0.1051-0.05720.20340.14950.01770.03810.2018-0.01630.156629.5672-26.13491.635
140.1378-0.0344-0.24540.4226-0.28470.6016-0.0288-0.06730.0429-0.01040.1193-0.038-0.07160.26180.1030.1235-0.00210.02050.2619-0.06920.197546.8996-33.118485.926
150.3914-0.37750.05630.3718-0.27671.12920.09850.01860.028-0.14950.0278-0.00040.05250.10450.21810.1571-0.01060.01910.1546-0.03110.166639.4379-36.889268.7281
160.0626-0.0577-0.06760.1393-0.05950.1256-0.0778-0.10090.03850.21320.19010.0622-0.16630.266500.50590.05570.03830.4672-0.00750.453729.772-46.5881113.8196
170.6609-0.1072-0.08220.49930.09090.2427-0.0378-0.02950.22380.0750.06630.05060.00290.04240.00320.15290.0562-0.04970.1803-0.01360.275625.266641.55959.5409
180.20860.12040.03280.1739-0.06250.0610.0240.0550.3169-0.01260.02880.04-0.04950.05970.00010.18410.0231-0.04450.251-0.03880.373632.955249.527857.7407
190.28150.13160.20240.7646-0.12820.27950.1453-0.46190.36870.41310.16910.1764-0.07570.05610.14990.3920.13060.01340.3744-0.26180.4418.545251.887381.701
200.1519-0.00940.02250.1078-0.10640.08950.0032-0.07610.4314-0.03460.02540.0143-0.00810.1426-0.00110.20930.0373-0.05470.2713-0.07760.455432.538156.078763.1876
210.343-0.0098-0.04870.32960.02180.1008-0.01420.01130.3355-0.00620.00720.1584-0.0824-0.0606-0.00610.18840.0727-0.04860.24410.00170.427617.302948.45655.0115
22-0.0155-0.0454-0.04250.22630.14620.0934-0.0527-0.08340.30290.2061-0.03660.09280.0208-0.127-0.08450.17470.1248-0.06090.25740.02890.43818.538844.172458.2577
230.0365-0.0518-0.07910.0650.07770.10720.0329-0.03890.36510.22470.08550.15980.0279-0.01980.02250.19270.13770.06170.2125-0.050.54231.445850.651971.5573
240.0199-0.0022-0.06430.16820.16030.2168-0.1242-0.11560.00670.33720.1310.18690.10840.0090.00450.25450.09680.02460.2443-0.00030.33815.216333.605569.4194
250.18280.05380.03720.16520.0181-0.011-0.08330.18660.3226-0.12840.2251-0.014-0.0340.0010.00010.3257-0.04-0.06280.39370.04160.363144.31532.494646.893
260.22040.17740.10870.2052-0.06660.3045-0.0543-0.0776-0.0209-0.15970.04480.03180.16820.0731-00.37560.04050.06830.22640.01490.305334.0995-76.358289.5565
27-0.0280.0309-0.07020.0607-0.03860.02780.0476-0.11890.0530.33130.091-0.0152-0.11260.1130.00010.39780.1625-0.05390.4958-0.01940.501250.5646-71.5555101.7924
280.15070.2442-0.05380.3535-0.07120.1054-0.0885-0.21060.0245-0.01930.01740.09010.2918-0.0694-00.34230.02620.07770.2840.06770.361328.28-81.3125101.6687
290.10480.039-0.15620.5872-0.00440.8545-0.1371-0.1713-0.2273-0.187-0.0701-0.18780.8190.0352-0.13130.39310.29610.11770.19110.14070.439745.4297-86.572596.8269
300.23130.2422-0.16770.5352-0.20240.0385-0.20230.0035-0.1732-0.30090.1325-0.16460.24660.04040.00560.52530.05270.10120.2499-0.04440.357443.4163-81.576578.3238
310.38260.1520.08590.2513-0.12340.1288-0.2693-0.0079-0.03870.06030.1532-0.36230.2455-0.0471-0.07360.40150.06950.06840.2765-0.05480.338153.2305-67.073380.1598
320.0832-0.1019-0.07780.2548-0.06830.0865-0.2450.0508-0.1394-0.01060.11480.29740.3094-0.1416-0.00010.5221-0.00980.05620.5689-0.02990.54618.2271-66.1501106.2826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 121 )A5 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 159 )A122 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 214 )A160 - 214
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 251 )A215 - 251
5X-RAY DIFFRACTION5chain 'A' and (resid 252 through 313 )A252 - 313
6X-RAY DIFFRACTION6chain 'A' and (resid 314 through 431 )A314 - 431
7X-RAY DIFFRACTION7chain 'A' and (resid 432 through 487 )A432 - 487
8X-RAY DIFFRACTION8chain 'A' and (resid 488 through 512 )A488 - 512
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 121 )B5 - 121
10X-RAY DIFFRACTION10chain 'B' and (resid 122 through 159 )B122 - 159
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 214 )B160 - 214
12X-RAY DIFFRACTION12chain 'B' and (resid 215 through 251 )B215 - 251
13X-RAY DIFFRACTION13chain 'B' and (resid 252 through 313 )B252 - 313
14X-RAY DIFFRACTION14chain 'B' and (resid 314 through 391 )B314 - 391
15X-RAY DIFFRACTION15chain 'B' and (resid 392 through 472 )B392 - 472
16X-RAY DIFFRACTION16chain 'B' and (resid 473 through 510 )B473 - 510
17X-RAY DIFFRACTION17chain 'C' and (resid 5 through 182 )C5 - 182
18X-RAY DIFFRACTION18chain 'C' and (resid 183 through 214 )C183 - 214
19X-RAY DIFFRACTION19chain 'C' and (resid 215 through 251 )C215 - 251
20X-RAY DIFFRACTION20chain 'C' and (resid 252 through 282 )C252 - 282
21X-RAY DIFFRACTION21chain 'C' and (resid 283 through 360 )C283 - 360
22X-RAY DIFFRACTION22chain 'C' and (resid 361 through 391 )C361 - 391
23X-RAY DIFFRACTION23chain 'C' and (resid 392 through 431 )C392 - 431
24X-RAY DIFFRACTION24chain 'C' and (resid 432 through 472 )C432 - 472
25X-RAY DIFFRACTION25chain 'C' and (resid 473 through 509 )C473 - 509
26X-RAY DIFFRACTION26chain 'D' and (resid 5 through 121 )D5 - 121
27X-RAY DIFFRACTION27chain 'D' and (resid 122 through 159 )D122 - 159
28X-RAY DIFFRACTION28chain 'D' and (resid 160 through 214 )D160 - 214
29X-RAY DIFFRACTION29chain 'D' and (resid 215 through 313 )D215 - 313
30X-RAY DIFFRACTION30chain 'D' and (resid 314 through 431 )D314 - 431
31X-RAY DIFFRACTION31chain 'D' and (resid 432 through 472 )D432 - 472
32X-RAY DIFFRACTION32chain 'D' and (resid 473 through 509 )D473 - 509

+
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