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- PDB-7v4z: Structure of Horcolin native form -

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Basic information

Entry
Database: PDB / ID: 7v4z
TitleStructure of Horcolin native form
ComponentsHorcolin
KeywordsSUGAR BINDING PROTEIN / Horcolin / mannose-binding lectin
Function / homology
Function and homology information


apoplast / mannose binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Horcolin
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsBobbili, K.B. / Sivaji, N. / Jayaprakash, N.G. / Narayanan, V. / Sekhar, A. / Suguna, K. / Surolia, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Biochemistry / Year: 2022
Title: Structure and Carbohydrate Recognition by the Nonmitogenic Lectin Horcolin.
Authors: Narayanan, V. / Bobbili, K.B. / Sivaji, N. / Jayaprakash, N.G. / Suguna, K. / Surolia, A. / Sekhar, A.
History
DepositionAug 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: 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
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Horcolin
C: Horcolin
B: Horcolin
D: Horcolin
E: Horcolin
F: Horcolin
G: Horcolin
H: Horcolin
I: Horcolin
J: Horcolin
K: Horcolin
L: Horcolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,38243
Polymers181,63312
Non-polymers2,74931
Water24,4641358
1
A: Horcolin
C: Horcolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,94910
Polymers30,2722
Non-polymers6778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Horcolin
D: Horcolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6416
Polymers30,2722
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Horcolin
F: Horcolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5485
Polymers30,2722
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Horcolin
H: Horcolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9319
Polymers30,2722
Non-polymers6597
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Horcolin
J: Horcolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5485
Polymers30,2722
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Horcolin
L: Horcolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7658
Polymers30,2722
Non-polymers4936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.179, 94.419, 238.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A C
21Chains A B
31Chains A D
41Chains A E
51Chains A F
61Chains A G
71Chains A H
81Chains A I
91Chains A J
101Chains A K
111Chains A L
121Chains C B
131Chains C D
141Chains C E
151Chains C F
161Chains C G
171Chains C H
181Chains C I
191Chains C J
201Chains C K
211Chains C L
221Chains B D
231Chains B E
241Chains B F
251Chains B G
261Chains B H
271Chains B I
281Chains B J
291Chains B K
301Chains B L
311Chains D E
321Chains D F
331Chains D G
341Chains D H
351Chains D I
361Chains D J
371Chains D K
381Chains D L
391Chains E F
401Chains E G
411Chains E H
421Chains E I
431Chains E J
441Chains E K
451Chains E L
461Chains F G
471Chains F H
481Chains F I
491Chains F J
501Chains F K
511Chains F L
521Chains G H
531Chains G I
541Chains G J
551Chains G K
561Chains G L
571Chains H I
581Chains H J
591Chains H K
601Chains H L
611Chains I J
621Chains I K
631Chains I L
641Chains J K
651Chains J L
661Chains K L

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Components

#1: Protein
Horcolin / Agglutinin / Mannose-specific lectin


Mass: 15136.077 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5U9T2
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→59.83 Å / Num. obs: 513816 / % possible obs: 96.8 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.9
Reflection shellResolution: 1.16→1.23 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 69425 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X1V
Resolution: 1.16→55.866 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.383 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1962 25278 4.921 %
Rwork0.1815 488415 -
all0.182 --
obs-513693 96.663 %
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: 14.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.228 Å20 Å20 Å2
2--0.246 Å2-0 Å2
3----0.475 Å2
Refinement stepCycle: LAST / Resolution: 1.16→55.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12444 0 179 1358 13981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01312856
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712018
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.64517410
X-RAY DIFFRACTIONr_angle_other_deg1.5731.57927789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07151709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26421.983484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.545151879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9711556
X-RAY DIFFRACTIONr_chiral_restr0.1030.21781
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022688
X-RAY DIFFRACTIONr_nbd_refined0.1620.21721
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.211308
X-RAY DIFFRACTIONr_nbtor_refined0.1670.26612
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1010.26755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2803
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1380.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.280.221
X-RAY DIFFRACTIONr_nbd_other0.2310.2100
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.231
X-RAY DIFFRACTIONr_mcbond_it0.7310.5996872
X-RAY DIFFRACTIONr_mcbond_other0.7290.5996871
X-RAY DIFFRACTIONr_mcangle_it1.0830.9028569
X-RAY DIFFRACTIONr_mcangle_other1.0840.9028570
X-RAY DIFFRACTIONr_scbond_it1.3020.7525984
X-RAY DIFFRACTIONr_scbond_other1.3020.7525985
X-RAY DIFFRACTIONr_scangle_it1.9271.0678841
X-RAY DIFFRACTIONr_scangle_other1.9271.0678842
X-RAY DIFFRACTIONr_lrange_it4.4328.43513508
X-RAY DIFFRACTIONr_lrange_other4.4318.43713509
X-RAY DIFFRACTIONr_ncsr_local_group_10.0990.054181
X-RAY DIFFRACTIONr_ncsr_local_group_20.0590.054284
X-RAY DIFFRACTIONr_ncsr_local_group_30.1060.054187
X-RAY DIFFRACTIONr_ncsr_local_group_40.0570.054310
X-RAY DIFFRACTIONr_ncsr_local_group_50.0980.054143
X-RAY DIFFRACTIONr_ncsr_local_group_60.1080.054179
X-RAY DIFFRACTIONr_ncsr_local_group_70.0720.054259
X-RAY DIFFRACTIONr_ncsr_local_group_80.0960.054181
X-RAY DIFFRACTIONr_ncsr_local_group_90.0730.054231
X-RAY DIFFRACTIONr_ncsr_local_group_100.1030.054154
X-RAY DIFFRACTIONr_ncsr_local_group_110.060.054272
X-RAY DIFFRACTIONr_ncsr_local_group_120.10.054122
X-RAY DIFFRACTIONr_ncsr_local_group_130.0620.054358
X-RAY DIFFRACTIONr_ncsr_local_group_140.10.054164
X-RAY DIFFRACTIONr_ncsr_local_group_150.0670.054298
X-RAY DIFFRACTIONr_ncsr_local_group_160.0930.054290
X-RAY DIFFRACTIONr_ncsr_local_group_170.1010.054197
X-RAY DIFFRACTIONr_ncsr_local_group_180.0790.054262
X-RAY DIFFRACTIONr_ncsr_local_group_190.0940.054215
X-RAY DIFFRACTIONr_ncsr_local_group_200.0910.054248
X-RAY DIFFRACTIONr_ncsr_local_group_210.0940.054199
X-RAY DIFFRACTIONr_ncsr_local_group_220.0960.054153
X-RAY DIFFRACTIONr_ncsr_local_group_230.0580.054312
X-RAY DIFFRACTIONr_ncsr_local_group_240.090.054170
X-RAY DIFFRACTIONr_ncsr_local_group_250.10.054146
X-RAY DIFFRACTIONr_ncsr_local_group_260.0660.054269
X-RAY DIFFRACTIONr_ncsr_local_group_270.0880.054215
X-RAY DIFFRACTIONr_ncsr_local_group_280.0630.054200
X-RAY DIFFRACTIONr_ncsr_local_group_290.0970.054184
X-RAY DIFFRACTIONr_ncsr_local_group_300.0650.054263
X-RAY DIFFRACTIONr_ncsr_local_group_310.1070.054174
X-RAY DIFFRACTIONr_ncsr_local_group_320.0610.054313
X-RAY DIFFRACTIONr_ncsr_local_group_330.0780.054368
X-RAY DIFFRACTIONr_ncsr_local_group_340.1030.054217
X-RAY DIFFRACTIONr_ncsr_local_group_350.0710.054314
X-RAY DIFFRACTIONr_ncsr_local_group_360.0940.054242
X-RAY DIFFRACTIONr_ncsr_local_group_370.0810.054299
X-RAY DIFFRACTIONr_ncsr_local_group_380.1020.054211
X-RAY DIFFRACTIONr_ncsr_local_group_390.0980.054182
X-RAY DIFFRACTIONr_ncsr_local_group_400.1040.054171
X-RAY DIFFRACTIONr_ncsr_local_group_410.0740.054295
X-RAY DIFFRACTIONr_ncsr_local_group_420.0970.054238
X-RAY DIFFRACTIONr_ncsr_local_group_430.0740.054210
X-RAY DIFFRACTIONr_ncsr_local_group_440.10.054207
X-RAY DIFFRACTIONr_ncsr_local_group_450.0610.054307
X-RAY DIFFRACTIONr_ncsr_local_group_460.0810.054278
X-RAY DIFFRACTIONr_ncsr_local_group_470.0980.054221
X-RAY DIFFRACTIONr_ncsr_local_group_480.0740.054310
X-RAY DIFFRACTIONr_ncsr_local_group_490.090.054196
X-RAY DIFFRACTIONr_ncsr_local_group_500.0810.054299
X-RAY DIFFRACTIONr_ncsr_local_group_510.0960.054221
X-RAY DIFFRACTIONr_ncsr_local_group_520.1030.054204
X-RAY DIFFRACTIONr_ncsr_local_group_530.0650.054333
X-RAY DIFFRACTIONr_ncsr_local_group_540.0910.054250
X-RAY DIFFRACTIONr_ncsr_local_group_550.0480.054360
X-RAY DIFFRACTIONr_ncsr_local_group_560.1020.054212
X-RAY DIFFRACTIONr_ncsr_local_group_570.0970.054277
X-RAY DIFFRACTIONr_ncsr_local_group_580.0690.054261
X-RAY DIFFRACTIONr_ncsr_local_group_590.1050.054248
X-RAY DIFFRACTIONr_ncsr_local_group_600.0510.054414
X-RAY DIFFRACTIONr_ncsr_local_group_610.090.054207
X-RAY DIFFRACTIONr_ncsr_local_group_620.0610.054380
X-RAY DIFFRACTIONr_ncsr_local_group_630.0930.054276
X-RAY DIFFRACTIONr_ncsr_local_group_640.0870.054209
X-RAY DIFFRACTIONr_ncsr_local_group_650.0550.054279
X-RAY DIFFRACTIONr_ncsr_local_group_660.1010.054249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.23517050.23432845X-RAY DIFFRACTION88.3496
1.226-1.2610.24316820.2433186X-RAY DIFFRACTION94.1742
1.261-1.30.24216950.23532480X-RAY DIFFRACTION95.015
1.3-1.3430.23916440.22431703X-RAY DIFFRACTION95.6241
1.343-1.390.216000.19330674X-RAY DIFFRACTION95.6749
1.39-1.4420.22215480.20829975X-RAY DIFFRACTION96.5897
1.442-1.5010.21114680.19529180X-RAY DIFFRACTION97.658
1.501-1.5680.19914340.18728180X-RAY DIFFRACTION98.4737
1.568-1.6450.1813480.16527059X-RAY DIFFRACTION98.5089
1.645-1.7340.19213790.18125781X-RAY DIFFRACTION98.994
1.734-1.8390.19412530.17324674X-RAY DIFFRACTION99.8844
1.839-1.9660.18512080.16623262X-RAY DIFFRACTION99.9428
1.966-2.1230.17410650.1621728X-RAY DIFFRACTION99.943
2.123-2.3260.17410890.16419941X-RAY DIFFRACTION99.9572
2.326-2.60.1879260.17118153X-RAY DIFFRACTION99.9948
2.6-3.0020.1858760.17416058X-RAY DIFFRACTION99.9882
3.002-3.6760.1897750.16813578X-RAY DIFFRACTION99.9652
3.676-5.1960.185280.16610705X-RAY DIFFRACTION99.8134
5.196-55.860.2653230.2266124X-RAY DIFFRACTION99.8142
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)
11.03810.1049-0.2450.8744-0.0451.41550.01760.00810.06510.0332-0.0317-0.053-0.04690.11810.0140.0298-0.0095-0.00170.0254-0.00290.04131.427315.540835.0863
21.10660.5762-0.07281.66010.19491.833-0.01380.13120.0668-0.0787-0.0160.10640.0851-0.01130.02980.03350.0035-0.00640.0395-0.0020.031624.78933.050114.2464
30.7861-0.03470.56811.22310.18063.50020.05820.046-0.0969-0.00590.0587-0.11920.33720.4951-0.11690.07980.0631-0.01060.0996-0.03090.062330.9125-14.772544.6441
40.9828-0.55280.39571.4459-0.56632.61910.0052-0.0864-0.05570.0960.00260.04-0.0670.1176-0.00780.0238-0.01030.00450.04270.00230.03322.9362-2.600365.1286
50.9457-0.39-0.02721.4188-0.29612.1675-0.0238-0.01660.0209-0.00260.06910.078-0.0491-0.2545-0.04530.03030.01330.00410.04650.0230.044240.2902-31.87174.0439
61.0655-0.5032-0.16411.6688-0.39592.1063-0.0038-0.13240.05870.07760.0633-0.08770.0019-0.1596-0.05950.03030.0068-0.01150.06430.02090.044446.9442-43.350325.4642
70.8508-0.17790.34341.2984-0.20541.37830.0515-0.005-0.01720.0299-0.0275-0.0646-0.14420.0185-0.0240.04850.00450.00290.0082-0.0150.07177.9824-29.695618.9079
80.86560.29330.26462.23940.58821.69610.00960.0041-0.0606-0.01960.0791-0.28660.03490.0973-0.08880.0265-0.00060.00120.007-0.00990.09215.2352-53.454414.4676
91.07390.1834-1.05461.5595-0.45072.4386-0.0057-0.00030.0214-0.0216-0.0035-0.0060.16650.0170.00920.0404-0.0035-0.0020.02130.02590.084762.5493-16.640260.0391
101.10990.1984-0.33191.7928-0.52871.92660.0292-0.00590.09050.13940.12530.2527-0.1787-0.195-0.15450.09310.03410.04440.04290.04450.11455.18286.948755.6727
110.97270.15630.40141.4676-0.08651.39390.03390.0168-0.03520.0366-0.01860.0689-0.06760.0176-0.01530.0225-0.00460.00160.00520.0130.072163.553617.577122.0854
120.9693-0.42250.27261.8719-0.41911.55340.0037-0.0081-0.0768-0.04790.05580.20560.0469-0.0839-0.05950.05-0.00310.00010.00550.00890.078356.1027-6.144726.0836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA3 - 204
2X-RAY DIFFRACTION2ALLC3 - 304
3X-RAY DIFFRACTION3ALLB4 - 301
4X-RAY DIFFRACTION4ALLD3 - 303
5X-RAY DIFFRACTION5ALLE4 - 302
6X-RAY DIFFRACTION6ALLF4 - 301
7X-RAY DIFFRACTION7ALLG3 - 305
8X-RAY DIFFRACTION8ALLH4 - 302
9X-RAY DIFFRACTION9ALLI4 - 302
10X-RAY DIFFRACTION10ALLJ3 - 301
11X-RAY DIFFRACTION11ALLK4 - 305
12X-RAY DIFFRACTION12ALLL4 - 301

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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