[English] 日本語
Yorodumi
- PDB-3zyf: CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH NPG AT 1.9 A RES... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zyf
TitleCRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH NPG AT 1.9 A RESOLUTION
ComponentsPA-I GALACTOPHILIC LECTIN
KeywordsSUGAR BINDING PROTEIN / ADHESIN / GLYCOSPHINGOLIPID-ANTIGEN / GALACTOSE-SPECIFIC / GALACTOSIDES
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
4-nitrophenyl beta-D-galactopyranoside / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 Å
AuthorsKadam, R.U. / Bergmann, M. / Hurley, M. / Garg, D. / Cacciarini, M. / Swiderska, M.A. / Nativi, C. / Sattler, M. / Smyth, A.R. / Williams, P. ...Kadam, R.U. / Bergmann, M. / Hurley, M. / Garg, D. / Cacciarini, M. / Swiderska, M.A. / Nativi, C. / Sattler, M. / Smyth, A.R. / Williams, P. / Camara, M. / Stocker, A. / Darbre, T. / Reymond, J.-L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: A Glycopeptide Dendrimer Inhibitor of the Galactose-Specific Lectin Leca and of Pseudomonas Aeruginosa Biofilms.
Authors: Kadam, R.U. / Bergmann, M. / Hurley, M. / Garg, D. / Cacciarini, M. / Swiderska, M.A. / Nativi, C. / Sattler, M. / Smyth, A.R. / Williams, P. / Camara, M. / Stocker, A. / Darbre, T. / Reymond, J.-L.
History
DepositionAug 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_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.pdbx_dist_value / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PA-I GALACTOPHILIC LECTIN
B: PA-I GALACTOPHILIC LECTIN
C: PA-I GALACTOPHILIC LECTIN
D: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,97112
Polymers51,6054
Non-polymers1,3658
Water7,044391
1
A: PA-I GALACTOPHILIC LECTIN
B: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4856
Polymers25,8032
Non-polymers6834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-13.8 kcal/mol
Surface area12800 Å2
MethodPISA
2
C: PA-I GALACTOPHILIC LECTIN
D: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4856
Polymers25,8032
Non-polymers6834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-14.7 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.562, 84.562, 163.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
PA-I GALACTOPHILIC LECTIN / LECTIN LECA / PA-IL / GALACTOSE-BINDING LECTIN


Mass: 12901.333 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET25PAIL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-147 / 4-nitrophenyl beta-D-galactopyranoside / 1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE / 4-nitrophenyl beta-D-galactoside / 4-nitrophenyl D-galactoside / 4-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C12H15NO8
IdentifierTypeProgram
1-O-[P-nitrophenyl]-b-D-galactopyranoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.81 Å3/Da / Density % sol: 56.3 % / Description: NONE
Crystal growpH: 7.5 / Details: 4.0 M SODIUM FORMATE., pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→48.28 Å / Num. obs: 44306 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OKO
Resolution: 1.944→48.284 Å / SU ML: 0.24 / σ(F): 2.04 / Phase error: 17.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 2216 5 %
Rwork0.1855 --
obs0.1867 44301 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.577 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.8314 Å20 Å20 Å2
2--1.8314 Å20 Å2
3----3.6628 Å2
Refinement stepCycle: LAST / Resolution: 1.944→48.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 88 391 4083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033784
X-RAY DIFFRACTIONf_angle_d0.7225180
X-RAY DIFFRACTIONf_dihedral_angle_d18.8151368
X-RAY DIFFRACTIONf_chiral_restr0.046564
X-RAY DIFFRACTIONf_plane_restr0.003684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9436-1.98590.26271270.21852416X-RAY DIFFRACTION93
1.9859-2.03210.2311380.20742607X-RAY DIFFRACTION100
2.0321-2.08290.24891350.20962575X-RAY DIFFRACTION100
2.0829-2.13920.22141380.19452613X-RAY DIFFRACTION100
2.1392-2.20220.23331360.1942596X-RAY DIFFRACTION100
2.2022-2.27330.21591380.19722606X-RAY DIFFRACTION100
2.2733-2.35450.23631370.19132604X-RAY DIFFRACTION99
2.3545-2.44880.23971360.19412599X-RAY DIFFRACTION100
2.4488-2.56020.20131390.18672639X-RAY DIFFRACTION100
2.5602-2.69520.22551380.18472608X-RAY DIFFRACTION100
2.6952-2.8640.21981380.18732633X-RAY DIFFRACTION100
2.864-3.08510.22961400.18792650X-RAY DIFFRACTION100
3.0851-3.39550.20281390.17472655X-RAY DIFFRACTION100
3.3955-3.88670.18661420.16222687X-RAY DIFFRACTION100
3.8867-4.89610.16851430.16152713X-RAY DIFFRACTION100
4.8961-48.29860.19511520.18412884X-RAY DIFFRACTION100
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)
11.99951.46930.60232.87271.07010.42230.359-0.52430.07661.0873-0.3335-0.25460.2429-0.2998-0.08040.2761-0.0204-0.02420.2450.02630.123811.5475-16.894119.0984
20.2922-0.1466-0.63251.07121.27811.6765-0.0314-0.06-0.1078-0.0527-0.11410.0153-0.03190.07470.11060.15370.00270.02660.07730.00620.15698.2809-13.181512.7345
33.72921.92982.21352.5842.03351.835-0.6371-0.5870.1194-0.8440.54390.1037-1.1127-0.1270.09390.3186-0.05720.08030.1077-0.03430.05165.34442.769218.4193
41.98651.45060.56321.10720.00742.9328-0.04320.2055-0.0650.69320.36660.3518-1.12550.1567-0.28660.40970.02710.0208-0.02460.06280.1452-0.76976.172612.1037
50.2855-0.1333-0.09210.9799-0.66010.51910.05880.014-0.0936-0.4399-0.13190.1497-0.13070.09050.07090.41250.00040.04350.03550.01750.08283.2264-1.32536.4363
60.0802-0.2277-0.15570.94340.45230.3983-0.11340.0495-0.2421-0.1396-0.1908-0.1804-0.00550.00140.28480.26520.00630.0580.0653-0.00260.15595.4635-13.33033.3548
70.4085-0.6124-0.03551.20030.5781.4362-0.39650.07030.0417-0.0562-0.26940.8692-0.33290.07380.39710.1182-0.0140.0860.0599-0.08860.1937-2.2991-17.33479.5393
80.50540.4775-0.22881.4675-0.19920.12570.02990.0576-0.0792-0.5178-0.1462-0.1418-0.05080.07590.12970.2262-0.00450.06380.1362-0.03780.18567.6404-19.65634.4025
90.67140.5235-0.48062.14230.3770.48070.59490.0913-0.1333-1.1309-0.2060.6159-0.04210.5121-0.22640.0544-0.16670.2105-0.04940.1155-0.085911.7408-1.419511.1036
100.565-0.0125-0.02491.17330.55170.35750.1014-0.0411-0.0140.2101-0.32230.41420.5003-0.04650.26880.3217-0.04570.06960.07650.01030.19692.7293-22.568816.6677
110.8916-1.69150.17334.4815-1.48281.22960.09640.1664-0.48780.1783-0.66180.97830.02610.27970.28020.1943-0.01180.06180.2709-0.21250.4305-14.028-15.473721.1097
12-0.0704-0.3933-0.01221.43590.38621.0746-0.08140.029-0.23990.1915-0.25060.51870.1977-0.0490.30650.2074-0.0270.11860.0629-0.04670.2718-10.3065-12.528227.6527
135.057-3.97792.25494.9105-2.00133.2381-0.42320.1839-0.43020.47260.29990.6775-1.18980.20850.18980.36060.0004-0.02120.0610.03520.1012-5.49593.228322.7755
140.95480.23160.32180.117-0.18362.0798-0.05560.01610.1013-0.56150.1575-0.0794-0.5655-0.1296-0.06060.3209-0.09430.0260.1485-0.05760.08650.80215.672629.2097
150.9243-0.40260.00290.1780.06890.2226-0.1814-0.1225-0.09570.30950.0765-0.0820.10860.00330.10030.22970.01710.02920.009-0.0210.0973-4.0146-1.631134.4803
165.03091.9866-2.9390.771-1.11862.091-0.0549-0.2528-0.79210.6652-0.4281-0.01720.30520.14210.49570.4357-0.02870.18430.1234-0.00090.2318-7.6367-13.495536.9649
170.66350.48520.26981.361-0.15930.2649-0.229-0.0908-0.13030.16570.0399-0.26590.5761-0.13750.27320.37180.00550.11950.10380.04360.1595-0.2674-18.14730.4924
182.0471-4.15581.13248.5252-1.95334.4979-0.6338-0.0759-0.75010.7593-0.41791.67951.27780.13750.6370.55060.04670.35760.08250.0490.3296-10.2945-19.410535.8166
190.0662-0.1049-0.25761.80761.53771.24780.1103-0.0737-0.21240.3129-0.36940.2440.3063-0.27650.30490.0884-0.00980.06780.0018-0.08110.1039-12.4294-0.53729.8667
200.81750.20410.13310.1833-0.47971.995-0.0862-0.15840.2321-0.6234-0.3473-0.38060.909-0.05720.42830.3946-0.01850.19940.1237-0.05130.283-6.0804-22.237523.2468
212.9793-1.2879-0.30961.2731.54832.7649-0.2547-0.48520.7928-0.3685-0.25820.07550.1434-0.1250.38520.23350.08240.08790.1114-0.01710.2403-45.169-1.7429.8776
220.9924-0.4959-0.21320.39460.35410.76640.15790.04010.0601-0.0705-0.14890.37540.11820.06340.00450.31530.02650.0380.046-0.01580.1058-37.7197-4.81139.6651
231.0320.2430.52830.32360.41370.69390.032-0.0374-0.07660.5587-0.24630.26120.2920.04650.19210.33920.00830.03260.05130.00210.2103-39.5979-20.534416.2418
241.3397-0.7953-1.59431.27262.01173.3602-0.1309-0.1465-0.40770.7651-0.12040.6337-0.32220.24120.29240.35590.04020.03070.04420.05950.192-30.8513-23.100318.4408
251.39440.7539-0.63510.45090.11372.370.0844-0.0158-0.3784-0.1673-0.2889-0.53650.39240.11930.21080.30970.06080.04190.09330.06390.2488-28.645-15.820111.6326
260.22250.2767-0.02630.61390.21020.20150.0311-0.003-0.116-0.1701-0.03990.13390.04070.025-0.00220.25220.01690.09070.1490.04590.2101-28.2246-3.92487.34
270.915-0.28540.49730.7307-0.28441.31080.40720.2144-0.18440.9567-0.1492-0.062-0.38960.1919-0.1590.312-0.05380.05240.09710.03370.0416-30.07140.659116.9049
281.00372.8469-0.03458.3701-0.1010.5130.72140.18490.65740.9419-0.1471.04280.2461-0.0789-0.48910.36510.09650.09420.01610.02390.0976-30.71991.99275.5372
290.4133-0.19790.26840.73310.35890.5919-0.0437-0.02590.1854-0.5289-0.19610.05860.00470.00070.19030.29840.06010.05280.0426-0.01040.1197-36.9266-16.77096.703
301.33420.42420.41971.7681-0.07590.65010.4375-0.01810.26830.571-0.3901-0.21660.08890.0092-0.05460.37980.03280.12070.06120.00550.2454-39.21424.932215.8343
311.8858-3.61822.20592.0023-4.02083.9292-0.14210.4717-0.09910.60730.37231.1801-0.89491.0571-0.07230.2736-0.05920.04410.1425-0.08190.1999-33.9879-0.716532.9264
321.5115-0.1037-1.00710.38810.62281.58390.158-0.16550.105-0.1202-0.1186-0.00170.03630.1976-0.04650.2633-0.001-0.01380.07010.01320.0831-41.1822-4.261333.2424
330.44860.05060.0153.55031.00010.3246-0.30350.1006-0.04440.0834-0.09150.09250.68480.10050.26710.35550.06910.14550.05570.06520.1598-37.9789-20.21627.7707
342.30.06750.77390.9531-0.02831.3426-0.37680.1683-1.5332-0.03350.5828-0.8643-0.18480.0141-0.16920.3727-0.0840.21230.0418-0.02340.5015-46.5133-23.389325.7177
351.02570.09020.49160.43020.34990.8634-0.33260.0331-0.05110.24060.07030.294-0.1601-0.0020.26460.27790.00560.13280.02210.01740.2308-49.3301-15.975931.9884
360.26770.0790.67981.56191.36032.6308-0.1831-0.07590.05840.1368-0.26650.51650.2787-0.01350.35280.2791-0.03180.03720.146-0.01080.2171-50.6602-4.035135.5392
372.2914-2.37951.74098.0384-1.2591.415-0.0456-0.4468-0.2054-1.09370.43980.8603-0.006-0.0746-0.30370.1794-0.0137-0.01630.06760.02290.1889-49.09550.194425.6812
381.2815-0.8298-0.74751.55861.52422.0831-0.0517-0.10340.13780.05520.0449-0.01830.2847-0.1563-0.05630.2597-0.04460.03750.1853-0.00950.1901-48.70682.16736.9008
390.17530.5998-0.50111.8361-0.860.6727-0.2773-0.18050.05370.55590.25140.28540.46540.1670.00460.45370.09560.05310.11580.06220.1424-41.0134-15.986837.0358
401.6951-1.2112-0.06750.9511-0.06620.44110.59180.03350.6079-0.4252-0.4469-0.5367-0.26330.0886-0.15030.3924-0.0050.05780.15590.03670.2583-40.43945.047426.7068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:5)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 6:36)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 37:46)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 47:51)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 52:66)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 67:76)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 77:89)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 90:95)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 96:112)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 113:121)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 1:5)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 6:36)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 37:46)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 47:51)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 52:66)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 67:76)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 77:89)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 90:95)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 96:112)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 113:121)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 1:5)
22X-RAY DIFFRACTION22(CHAIN C AND RESID 6:36)
23X-RAY DIFFRACTION23(CHAIN C AND RESID 37:46)
24X-RAY DIFFRACTION24(CHAIN C AND RESID 47:51)
25X-RAY DIFFRACTION25(CHAIN C AND RESID 52:66)
26X-RAY DIFFRACTION26(CHAIN C AND RESID 67:76)
27X-RAY DIFFRACTION27(CHAIN C AND RESID 77:89)
28X-RAY DIFFRACTION28(CHAIN C AND RESID 90:95)
29X-RAY DIFFRACTION29(CHAIN C AND RESID 96:112)
30X-RAY DIFFRACTION30(CHAIN C AND RESID 113:121)
31X-RAY DIFFRACTION31(CHAIN D AND RESID 1:5)
32X-RAY DIFFRACTION32(CHAIN D AND RESID 6:36)
33X-RAY DIFFRACTION33(CHAIN D AND RESID 37:46)
34X-RAY DIFFRACTION34(CHAIN D AND RESID 47:51)
35X-RAY DIFFRACTION35(CHAIN D AND RESID 52:66)
36X-RAY DIFFRACTION36(CHAIN D AND RESID 67:76)
37X-RAY DIFFRACTION37(CHAIN D AND RESID 77:89)
38X-RAY DIFFRACTION38(CHAIN D AND RESID 90:95)
39X-RAY DIFFRACTION39(CHAIN D AND RESID 96:112)
40X-RAY DIFFRACTION40(CHAIN D AND RESID 113:121)

+
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://pdbjlvh1.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