[English] 日本語
Yorodumi
- PDB-6s5p: Cfucosylated peptide SBL2 bound to Fucose binding Lectin LecB (PA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s5p
TitleCfucosylated peptide SBL2 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.46 Angstrom resolution
Components
  • Fucose-binding lectin
  • SBL2
KeywordsSUGAR BINDING PROTEIN / Lectin / Fucosylated
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Calcium-mediated lectin / Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-ZDC / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Acs Chem.Biol. / Year: 2019
Title: X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.
Authors: Baeriswyl, S. / Gan, B.H. / Siriwardena, T.N. / Visini, R. / Robadey, M. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.L.
#1: Journal: Helv.Chim.Acta / Year: 2019
Title: X-Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB
Authors: Baeriswyl, S. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.-L.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _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.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.value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fucose-binding lectin
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
H: SBL2
E: SBL2
F: SBL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,38119
Polymers49,2367
Non-polymers1,14512
Water7,404411
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-96 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.099, 56.264, 70.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-454-

HOH

-
Components

#1: Protein
Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL


Mass: 11865.905 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fucose binding lectin LecB (PA-LII) from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Protein/peptide SBL2


Mass: 590.759 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: SBL2 N-terminally fucosylated peptide linker / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-ZDC / 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid


Type: D-saccharide / Mass: 206.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H14O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50% v/v (+/-)-2-Methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000033 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 1.46→46.365 Å / Num. obs: 164044 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.168 / Net I/σ(I): 9.95
Reflection shellResolution: 1.46→1.467 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 26246 / CC1/2: 0.529 / Rrim(I) all: 1.801 / % possible all: 98.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.63 Å46.37 Å
Translation2.63 Å46.37 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.1phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.46→46.365 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.25 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 8222 5.02 %
Rwork0.1766 155666 -
obs0.1775 163888 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.29 Å2 / Biso mean: 23.7699 Å2 / Biso min: 12.86 Å2
Refinement stepCycle: final / Resolution: 1.46→46.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 118 411 3869
Biso mean--30.36 33.94 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143435
X-RAY DIFFRACTIONf_angle_d0.9144703
X-RAY DIFFRACTIONf_chiral_restr0.093600
X-RAY DIFFRACTIONf_plane_restr0.004622
X-RAY DIFFRACTIONf_dihedral_angle_d18.7141131
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 (%)
1.4599-1.47650.41842580.40784946520494
1.4765-1.49390.38892710.391451505421100
1.4939-1.51210.38072790.36852075486100
1.5121-1.53120.36522740.338252205494100
1.5312-1.55140.31672740.311651745448100
1.5514-1.57260.31282800.308952155495100
1.5726-1.59510.31352720.282651645436100
1.5951-1.61890.2862740.282752125486100
1.6189-1.64420.27962720.271952075479100
1.6442-1.67120.27712790.268252185497100
1.6712-1.70.2772690.251751595428100
1.7-1.73090.27362780.237752155493100
1.7309-1.76420.24962760.226952165492100
1.7642-1.80020.23882800.21751755455100
1.8002-1.83940.22112750.206752045479100
1.8394-1.88220.22472710.197652025473100
1.8822-1.92920.18342780.176851925470100
1.9292-1.98140.21212760.163951735449100
1.9814-2.03970.15892720.162151805452100
2.0397-2.10550.19332720.164552315503100
2.1055-2.18080.1962730.165251945467100
2.1808-2.26810.16552680.145651955463100
2.2681-2.37130.16232800.142252095489100
2.3713-2.49630.14222790.137451715450100
2.4963-2.65270.14642760.136452135489100
2.6527-2.85750.13982730.130651845457100
2.8575-3.1450.17612760.129952205496100
3.145-3.60.14662740.126952005474100
3.6-4.5350.1672670.138152115478100
4.535-46.38850.18552760.1952095485100
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)
10.29510.15660.01550.9888-0.40440.89090.01180.01270.0214-0.1412-0.0187-0.00040.0952-0.0250.00690.27740.00440.00230.1576-0.00530.1628-29.74658.6715-29.4385
20.27180.3031-0.42081.7582-0.97191.0121-0.01470.07260.0242-0.2460.0204-0.00030.0975-0.0622-0.00520.3116-0.0114-0.01660.1697-0.00760.157-28.588111.3541-33.4898
35.28711.43215.38433.062.6085.96850.2942-0.2216-0.364-0.0557-0.20130.66750.3613-0.39370.09110.277-0.0037-0.02260.1821-0.01170.2166-42.53374.4824-24.528
40.40720.36980.09390.56820.08460.210.0268-0.01850.0806-0.0098-0.01060.0374-0.0107-0.0127-0.01360.2710.00220.0020.154800.1671-26.169812.9555-22.1128
54.59774.7264-2.14156.1364-2.26871.65830.0807-0.1579-0.02080.0759-0.1158-0.1462-0.00340.02510.02930.25720.00990.00120.1543-0.00480.1867-13.97739.2809-8.605
60.9107-0.1478-0.91471.2479-0.48175.6681-0.03490.0316-0.1198-0.0383-0.0096-0.14730.31060.23950.06770.25170.01850.00590.1131-0.01380.1968-10.25952.9154-22.4981
70.98180.5432-2.99461.4649-0.69289.9027-0.1495-0.1271-0.1727-0.1155-0.0852-0.14720.78040.28810.24230.28880.01880.01050.15050.00160.2057-16.113-1.4099-19.3207
84.55341.3708-4.5890.6134-0.62177.20080.0196-0.4333-0.11350.1085-0.1098-0.15640.00040.45010.07950.30840.0244-0.01080.19260.01460.2124-9.55355.1647-10.7866
95.354-5.4532-1.51146.31493.04843.39050.31590.59750.3503-0.7311-0.055-1.21480.35210.6243-0.32620.3330.05860.09410.2581-0.02410.3411.79337.88-24.9315
101.1848-0.7889-0.52040.97870.63930.74430.0331-0.00460.0358-0.0555-0.0082-0.1072-0.02530.0441-0.01360.24630.00680.01120.1494-0.00370.1785-14.306714.4894-20.4189
112.71811.233-2.56290.716-1.28622.505-0.07180.00480.0449-0.19670.08270.02880.16740.00360.01110.24890.00610.01070.1373-0.00450.1638-20.38985.9932-16.8724
123.82430.8143.92340.33011.31075.98660.0071-0.0533-0.176-0.01930.0371-0.03560.0082-0.0521-0.04770.26850.0050.02090.14060.00140.169-28.864219.1377-3.418
132.4513-2.14291.42133.5521-2.6922.1609-0.0493-0.04270.19870.0989-0.0691-0.0996-0.1823-0.06450.19570.29850.01440.02340.1325-0.0230.1713-29.88234.7097-7.749
140.03770.3594-0.40762.2009-2.55943.26180.0103-0.0229-0.00270.25790.0640.278-0.1766-0.1107-0.14470.3020.02320.01810.16640.0040.2048-35.597530.4785-0.9693
153.8169-2.5157-0.27672.49471.01281.9569-0.01070.16360.4308-0.17990.0518-0.069-0.38980.0228-0.12160.32950.00470.00680.14790.00550.2083-31.508142.5485-14.7715
161.3991-2.55573.50884.7169-6.37178.679-0.0136-0.0741-0.00990.50240.08070.3012-0.53-0.0038-0.06010.29610.01420.01630.1571-0.01460.1711-26.889433.962-0.5581
173.3967-2.54775.08323.7637-4.71858.06260.0516-0.2327-0.0973-0.00730.1320.19180.0823-0.3084-0.32860.2710.0170.03270.17290.00650.1882-33.351523.1268-1.1436
184.23254.18661.6824.3191.35751.80430.14760.06170.65480.6365-0.09511.4347-0.4896-0.5164-0.06460.32780.03860.07210.1894-0.00070.3416-44.736832.718-10.7063
191.8147-0.83720.02691.0492-0.04990.1468-0.0818-0.007-0.01370.0550.05740.0494-0.10090.0050.03130.24190.00630.01170.14370.00080.1621-24.69722.9797-11.3675
201.3896-0.7795-0.43231.9516-0.08880.99490.08280.1547-0.2301-0.2535-0.06740.1379-0.0373-0.10320.00840.25170.0283-0.02920.1801-0.0090.2019-37.803632.3464-20.5585
212.4966-1.28081.21960.7485-0.86991.26880.0612-0.07640.01490.00510.02250.0853-0.0260.0483-0.07220.26010.00760.01390.1466-0.00020.1702-22.699827.8603-5.3526
225.7314-3.92152.96115.4276-2.57182.49650.09050.15990.0291-0.2892-0.0682-0.09670.18820.0266-0.02990.2714-0.00970.01710.15330.00720.1538-15.118331.3104-24.8667
231.30830.22561.72770.8603-0.22937.02120.01220.00390.1568-0.0935-0.01160.028-0.14380.23770.02530.2814-0.00410.02240.1079-0.01440.1972-13.140837.8833-13.3867
243.0288-2.04910.57352.25060.94832.17080.00040.18820.1136-0.2834-0.0689-0.039-1.15670.06670.02280.3316-0.0437-0.00440.13620.00090.2213-10.764943.2245-15.7852
259.14771.64566.04166.3121.55154.04430.1102-0.37310.15920.52470.05390.185-0.0868-0.1279-0.14070.2853-0.0240.04940.1987-0.02930.1775-15.018436.0860.8572
262.299-0.62372.63211.2483-0.23.6402-0.10720.02070.208-0.1043-0.0038-0.0294-0.79020.21710.30030.3085-0.00550.01010.1206-0.00730.2067-19.180342.0425-14.7919
274.8075-0.93154.790.1943-0.8616.4162-0.07580.32440.2835-0.1544-0.1333-0.11270.12160.32630.32280.2976-0.02290.02660.1670.0310.1994-11.396136.0567-22.6647
288.68825.91483.14495.13244.57756.54440.3462-0.0946-0.22250.8264-0.0578-0.36250.327-0.0047-0.25090.2659-0.0019-0.01770.13230.01010.2145-0.533834.8993-8.0242
290.340.1649-0.03070.11630.05180.27180.0151-0.0290.0291-0.045-0.0041-0.0061-0.0676-0.0059-0.00050.24480.0010.00690.1405-0.00150.1731-17.147228.4182-13.9995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )A1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 68 )A49 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 74 )A69 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 114 )A75 - 114
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 12 )B1 - 12
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 48 )B13 - 48
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 56 )B49 - 56
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 68 )B57 - 68
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 74 )B69 - 74
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 104 )B75 - 104
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 114 )B105 - 114
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 12 )C1 - 12
13X-RAY DIFFRACTION13chain 'C' and (resid 13 through 25 )C13 - 25
14X-RAY DIFFRACTION14chain 'C' and (resid 26 through 42 )C26 - 42
15X-RAY DIFFRACTION15chain 'C' and (resid 43 through 48 )C43 - 48
16X-RAY DIFFRACTION16chain 'C' and (resid 49 through 56 )C49 - 56
17X-RAY DIFFRACTION17chain 'C' and (resid 57 through 68 )C57 - 68
18X-RAY DIFFRACTION18chain 'C' and (resid 69 through 74 )C69 - 74
19X-RAY DIFFRACTION19chain 'C' and (resid 75 through 95 )C75 - 95
20X-RAY DIFFRACTION20chain 'C' and (resid 96 through 104 )C96 - 104
21X-RAY DIFFRACTION21chain 'C' and (resid 105 through 114 )C105 - 114
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 12 )D1 - 12
23X-RAY DIFFRACTION23chain 'D' and (resid 13 through 34 )D13 - 34
24X-RAY DIFFRACTION24chain 'D' and (resid 35 through 42 )D35 - 42
25X-RAY DIFFRACTION25chain 'D' and (resid 43 through 48 )D43 - 48
26X-RAY DIFFRACTION26chain 'D' and (resid 49 through 56 )D49 - 56
27X-RAY DIFFRACTION27chain 'D' and (resid 57 through 68 )D57 - 68
28X-RAY DIFFRACTION28chain 'D' and (resid 69 through 74 )D69 - 74
29X-RAY DIFFRACTION29chain 'D' and (resid 75 through 114 )D75 - 114

+
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