[English] 日本語
Yorodumi
- PDB-5ltv: LIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ltv
TitleLIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID CHEMORECPETOR PCTC IN COMPLEX WITH GABA
ComponentsChemotactic transducer PctC
KeywordsSIGNALING PROTEIN / Ligand binding domain / Pseudomonas aeruginosa / chemotactic transducer
Function / homology
Function and homology information


amino acid binding / response to amino acid / chemotaxis / membrane => GO:0016020 / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain ...Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
GAMMA-AMINO-BUTANOIC ACID / ACETATE ION / Chemotactic transducer PctC / Methyl-accepting chemotaxis protein PctC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / Resolution: 2.31 Å
AuthorsGavira, J.A. / Rico-Jimenez, M. / Conejero-Muriel, M. / Krell, T.
Funding support Spain, 1items
OrganizationGrant numberCountry
MICINNBIO2013-4297-P Spain
CitationJournal: Mbio / Year: 2020
Title: How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Authors: Gavira, J.A. / Jimenez-Rico, M. / Pineda-Molina, E. / Krell, T.
History
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chemotactic transducer PctC
B: Chemotactic transducer PctC
C: Chemotactic transducer PctC
D: Chemotactic transducer PctC
E: Chemotactic transducer PctC
F: Chemotactic transducer PctC
G: Chemotactic transducer PctC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,38234
Polymers207,9877
Non-polymers2,39527
Water12,683704
1
A: Chemotactic transducer PctC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1966
Polymers29,7121
Non-polymers4835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chemotactic transducer PctC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2888
Polymers29,7121
Non-polymers5757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chemotactic transducer PctC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9644
Polymers29,7121
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chemotactic transducer PctC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9123
Polymers29,7121
Non-polymers1992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Chemotactic transducer PctC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0675
Polymers29,7121
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Chemotactic transducer PctC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9604
Polymers29,7121
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Chemotactic transducer PctC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9974
Polymers29,7121
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.765, 209.765, 68.885
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

-
Components

-
Protein , 1 types, 7 molecules ABCDEFG

#1: Protein
Chemotactic transducer PctC


Mass: 29712.447 Da / Num. of mol.: 7 / Fragment: ligand binding domain, UNP residues 30-281
Source method: isolated from a genetically manipulated source
Details: Ligand binding region of the PctC / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PAMH19_3853 / Plasmid: PET28B PLUS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A080VJ62, UniProt: Q9HW93*PLUS

-
Non-polymers , 5 types, 731 molecules

#2: Chemical
ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 8.5
Details: Capillary counter diffusion: 2.0M NH4 Sulphate,0.1M Tris-HCl pH 8.50.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.31→48.63 Å / Num. obs: 76088 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.162 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.31-2.396.61.0820.5571100
8.95-48.6370.0460.998198.1

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
SCALA0.5.21data scaling
SHELXphasing
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T65
Resolution: 2.31→48.63 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 3820 5.02 %Random
Rwork0.1772 ---
obs0.1796 76048 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.19 Å2 / Biso mean: 45.2512 Å2 / Biso min: 15.58 Å2
Refinement stepCycle: final / Resolution: 2.31→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11516 0 163 704 12383
Biso mean--61.34 44.16 -
Num. residues----1516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212347
X-RAY DIFFRACTIONf_angle_d1.22116844
X-RAY DIFFRACTIONf_chiral_restr0.061894
X-RAY DIFFRACTIONf_plane_restr0.0082201
X-RAY DIFFRACTIONf_dihedral_angle_d14.8177337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.33920.30361610.256926542815100
2.3392-2.370.29221670.241626372804100
2.37-2.40250.28261340.236526682802100
2.4025-2.43680.3221470.242326262773100
2.4368-2.47320.30951530.233826472800100
2.4732-2.51180.29271450.229726582803100
2.5118-2.5530.2561390.220426882827100
2.553-2.5970.27111380.210226432781100
2.597-2.64420.2621400.208726732813100
2.6442-2.69510.25191380.203626612799100
2.6951-2.75010.27791400.203726642804100
2.7501-2.80990.28361450.202726312776100
2.8099-2.87530.26581350.227252860100
2.8753-2.94710.2461480.198626472795100
2.9471-3.02680.24531340.185926752809100
3.0268-3.11590.24381220.185226842806100
3.1159-3.21640.26461470.186726722819100
3.2164-3.33140.22661400.182126802820100
3.3314-3.46470.21991340.170326742808100
3.4647-3.62230.22781320.165426922824100
3.6223-3.81320.18341420.152526642806100
3.8132-4.05210.18531260.137926992825100
4.0521-4.36470.18261580.135326502808100
4.3647-4.80360.1651370.131327102847100
4.8036-5.49790.19761310.151227092840100
5.4979-6.92360.19981280.1827432871100
6.9236-48.64070.21211590.18672754291399
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)
10.23820.13080.1115-0.00310.03830.0420.03590.15680.20410.04-0.03020.0674-0.10190.0625-0.0520.20180.10460.00420.39430.07390.290322.671568.741453.1476
20.0256-0.01150.00320.0056-0.00520.0025-0.18540.0365-0.17610.2890.190.05240.0221-0.0098-0.00010.29030.0902-0.02620.36430.02350.284519.321263.461584.294
30.235-0.1441-0.05120.1380.02920.2175-0.0156-0.03510.09840.1343-0.0028-0.1039-0.01730.02890.00010.19690.0461-0.02390.26090.00990.312231.006467.220876.5124
40.13890.0681-0.10590.1628-0.13260.14280.01990.08030.07110.06370.0391-0.1094-0.0152-0.1304-00.2160.05430.00260.28890.05110.310429.742770.135368.3757
50.03490.0097-0.04490.0724-0.09020.14880.12810.24820.2716-0.1390.2459-0.4171-0.02730.02950.00010.3230.00750.07020.3360.09460.44436.606871.294650.8735
60.0094-0.0136-0.03120.05820.06980.08410.074-0.2627-0.047-0.45580.324-0.3265-0.43320.1717-0.00030.4613-0.01670.12010.47110.00110.583141.873177.191749.4663
70.09150.10270.12250.13740.14260.16220.04650.47930.46870.0820.5370.196-0.4612-0.0720.1370.41080.01750.10850.55610.15790.326731.871175.721645.0179
80.20950.1811-0.05380.2156-0.11480.1673-0.0352-0.01260.0334-0.2526-0.0639-0.1424-0.3080.1151-0.00260.2546-0.0302-0.01540.3139-0.01040.3161-16.004660.385134.0073
90.03560.00250.04130.00560.01620.04950.2791-0.54750.0680.1796-0.0898-0.02850.0565-0.0980.00030.2436-0.08680.00360.42920.0060.3599-19.604263.209561.4686
100.09880.07260.00280.0716-0.02830.00910.16380.01990.141-0.1086-0.07620.1675-0.0011-0.07540.00520.172-0.0248-0.01820.27030.03190.3198-23.48659.930149.6621
110.10240.03380.10490.11950.11740.19150.1071-0.2026-0.18860.10360.00770.01140.12980.0342-0.00020.2226-0.0245-0.06360.31590.0510.3552-19.522647.663854.6327
120.0551-0.06430.05680.0993-0.0130.1472-0.0483-0.0349-0.3211-0.19350.1863-0.12140.2130.11900.2809-0.0468-0.04010.3202-0.04530.4859-18.884647.596943.2816
130.19420.1712-0.20960.076-0.13140.1864-0.0433-0.1708-0.1099-0.05330.03350.05390.0689-0.0709-0.04840.2046-0.0377-0.04570.2512-0.00410.2804-17.069554.134245.6479
140.0367-0.0109-0.06930.0817-0.03630.1289-0.18560.235-0.2127-0.24850.2426-0.06440.3074-0.1449-0.00010.55-0.02360.01870.3339-0.05960.4093-21.269843.390327.8401
15-0.00320.00080.00180.0021-0.0007-0.00220.33980.0578-0.0408-0.21080.1252-0.32830.7662-0.0873-0.00160.8268-0.2569-0.01771.0116-0.32750.7445-15.606539.969917.8236
160.02610.0186-0.02190.1116-0.01530.016-0.3840.0148-0.0175-0.40330.2777-0.3711-0.03810.2563-0.00510.5207-0.01850.02010.5005-0.14750.3537-14.514950.140423.9811
170.0923-0.02780.05510.40840.08160.04760.09590.17760.0917-0.00070.06810.1049-0.00090.11660.12920.07260.0125-0.05510.52390.09380.119118.535259.169153.0312
180.3737-0.11510.29670.2292-0.16470.35080.0764-0.2586-0.0557-0.0371-0.04220.20710.0899-0.26370.03590.1536-0.0103-0.04040.36740.04450.26921.238157.318270.8102
190.26320.1392-0.03650.19810.15960.3810.14060.238-0.0266-0.0503-0.09480.01370.0052-0.11030.00110.2470.0241-0.03350.38360.05320.24946.863757.19659.2722
200.3859-0.0155-0.22880.2110.2660.5480.10320.6577-0.4627-0.1471-0.17520.03380.0285-0.0221-0.01090.32250.14550.01250.8384-0.06930.153510.990254.892437.7357
210.2667-0.222-0.16980.2993-0.03310.19040.1187-0.06020.09610.0884-0.11060.0617-0.1543-0.0948-0.01350.27050.0563-0.01330.26790.00720.23477.115995.275816.105
220.2615-0.28650.01390.44270.00860.21140.0205-0.06310.0045-0.0106-0.02950.03290.18850.2146-0.04940.2730.053-0.02930.29720.01740.265815.260783.699819.8028
230.51510.2192-0.46220.3836-0.1590.36890.03820.11570.1133-0.0257-0.0178-0.00860.16690.10450.03790.24690.0551-0.02190.29120.00340.224610.192891.16459.8648
240.1459-0.0563-0.08240.1031-0.03320.09620.06330.3310.014-0.3771-0.0814-0.02110.19380.19510.00010.38430.06740.01640.3876-0.02120.297916.491289.2069-6.9337
250.23160.186-0.07310.1345-0.08750.07510.16420.21070.0825-0.1310.0833-0.02480.0342-0.07550.00540.26630.0765-0.03390.3530.01770.177912.264498.4859-8.4489
260.26010.1043-0.02220.0971-0.04950.15250.0804-0.0008-0.0891-0.05410.0768-0.01170.2697-0.1271-0.00130.3101-0.0779-0.00860.24040.00120.2222-21.974368.011930.2644
270.02150.00970.02240.01130.00150.0604-0.3752-0.33030.25980.47830.07760.0190.10090.2576-0.00060.4227-0.0257-0.04910.3352-0.06670.3181-13.636377.386757.8523
280.1565-0.0088-0.030.2133-0.08240.19550.0876-0.01270.0390.0999-0.1341-0.0261-0.10910.0667-0.00010.2516-0.03290.01440.25620.01450.2646-13.326583.429645.7482
290.01110.0096-0.02710.15920.02820.0219-0.26130.0116-0.0024-0.11110.2006-0.0796-0.0867-0.1026-0.00040.34120.00850.10460.47340.04760.316-15.644481.759532.9008
300.16860.02630.12380.10360.00260.0856-0.216-0.0767-0.0996-0.0253-0.17160.0730.0399-0.044-0.00440.224-0.02330.03070.3151-0.02210.2246-20.832579.900646.3049
310.00770.06010.07360.20760.04090.2880.11310.18380.0515-0.4272-0.0417-0.2051-0.19270.3417-00.39740.00940.0460.38230.02960.1804-15.451277.034418.0065
320.23410.08650.16960.22850.08950.12310.0730.1186-0.004-0.31790.01860.1834-0.2126-0.30420.05080.48220.0288-0.04610.4486-0.01570.1897-25.145375.740813.9627
330.4142-0.420.09650.21570.0720.39090.2615-0.0061-0.11680.0069-0.04960.07890.0250.09080.05120.25450.0383-0.01740.2643-0.00290.288-2.489697.506618.4749
340.16820.03920.20290.443-0.22250.38080.098-0.01470.11730.17090.05870.115-0.2005-0.10110.07740.24180.00160.08660.32570.04390.3215-7.8144106.039932.4789
350.0830.01870.09830.02160.07340.24710.0571-0.0031-0.02730.1626-0.027-0.0899-0.193-0.4872-0.00650.40280.022-0.09830.29260.05570.4568-11.7836105.568119.7671
360.00970.0340.04640.03440.08610.1823-0.0713-0.0244-0.06070.09810.0872-0.0157-0.0703-0.0957-00.24120.01920.04440.31760.0430.3206-8.435597.947929.259
370.0741-0.00070.01130.16760.03750.04210.28010.29520.1475-0.0286-0.07230.1141-0.05810.19670.01530.29690.0202-0.01940.44710.0870.2331-5.7975109.83842.0156
380.0995-0.02490.11020.14130.01850.1162-0.02980.08020.023-0.26370.05340.22260.0127-0.0740.01440.22420.02880.00210.28010.05810.3431-16.6616113.00826.7497
390.0419-0.05590.01470.07450.0060.0271-0.00680.5266-0.0589-0.1042-0.13630.43620.11170.079-0.02860.6833-0.1666-0.32630.65850.14730.5821-21.213107.1908-5.8341
400.1148-0.08020.00470.1120.07870.08410.33030.2537-0.147-0.1810.01430.22670.2003-0.0942-0.00020.39050.0841-0.03940.31370.03320.3123-13.8088101.98351.5857
410.3854-0.14540.02990.3892-0.21880.2184-0.2027-0.11620.0455-0.04010.18890.05470.17250.2030.00650.18590.10580.01650.32450.02660.274850.896595.612319.2278
420.642-0.04270.30380.46290.01880.57350.01550.1710.1201-0.06920.06690.1068-0.1086-0.02690.00010.22880.0116-0.00850.25890.03860.306440.976498.42940.5108
431.14580.64260.07680.96390.16830.9043-0.9694-0.2179-0.0749-0.21740.08330.4310.15780.017-0.77680.08470.23050.23590.2968-0.13940.42439.4006100.91828.9445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 76 )A40 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 90 )A77 - 90
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 138 )A91 - 138
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 186 )A139 - 186
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 211 )A187 - 211
6X-RAY DIFFRACTION6chain 'A' and (resid 212 through 232 )A212 - 232
7X-RAY DIFFRACTION7chain 'A' and (resid 233 through 265 )A233 - 265
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 77 )B44 - 77
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 90 )B78 - 90
10X-RAY DIFFRACTION10chain 'B' and (resid 91 through 106 )B91 - 106
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 138 )B107 - 138
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 155 )B139 - 155
13X-RAY DIFFRACTION13chain 'B' and (resid 156 through 186 )B156 - 186
14X-RAY DIFFRACTION14chain 'B' and (resid 187 through 222 )B187 - 222
15X-RAY DIFFRACTION15chain 'B' and (resid 223 through 244 )B223 - 244
16X-RAY DIFFRACTION16chain 'B' and (resid 245 through 266 )B245 - 266
17X-RAY DIFFRACTION17chain 'C' and (resid 41 through 77 )C41 - 77
18X-RAY DIFFRACTION18chain 'C' and (resid 78 through 138 )C78 - 138
19X-RAY DIFFRACTION19chain 'C' and (resid 139 through 188 )C139 - 188
20X-RAY DIFFRACTION20chain 'C' and (resid 189 through 265 )C189 - 265
21X-RAY DIFFRACTION21chain 'D' and (resid 41 through 90 )D41 - 90
22X-RAY DIFFRACTION22chain 'D' and (resid 91 through 155 )D91 - 155
23X-RAY DIFFRACTION23chain 'D' and (resid 156 through 201 )D156 - 201
24X-RAY DIFFRACTION24chain 'D' and (resid 202 through 232 )D202 - 232
25X-RAY DIFFRACTION25chain 'D' and (resid 233 through 266 )D233 - 266
26X-RAY DIFFRACTION26chain 'E' and (resid 41 through 77 )E41 - 77
27X-RAY DIFFRACTION27chain 'E' and (resid 78 through 90 )E78 - 90
28X-RAY DIFFRACTION28chain 'E' and (resid 91 through 138 )E91 - 138
29X-RAY DIFFRACTION29chain 'E' and (resid 139 through 155 )E139 - 155
30X-RAY DIFFRACTION30chain 'E' and (resid 156 through 178 )E156 - 178
31X-RAY DIFFRACTION31chain 'E' and (resid 179 through 222 )E179 - 222
32X-RAY DIFFRACTION32chain 'E' and (resid 223 through 266 )E223 - 266
33X-RAY DIFFRACTION33chain 'F' and (resid 41 through 90 )F41 - 90
34X-RAY DIFFRACTION34chain 'F' and (resid 91 through 138 )F91 - 138
35X-RAY DIFFRACTION35chain 'F' and (resid 139 through 155 )F139 - 155
36X-RAY DIFFRACTION36chain 'F' and (resid 156 through 178 )F156 - 178
37X-RAY DIFFRACTION37chain 'F' and (resid 179 through 201 )F179 - 201
38X-RAY DIFFRACTION38chain 'F' and (resid 202 through 222 )F202 - 222
39X-RAY DIFFRACTION39chain 'F' and (resid 223 through 243 )F223 - 243
40X-RAY DIFFRACTION40chain 'F' and (resid 244 through 266 )F244 - 266
41X-RAY DIFFRACTION41chain 'G' and (resid 42 through 77 )G42 - 77
42X-RAY DIFFRACTION42chain 'G' and (resid 78 through 177 )G78 - 177
43X-RAY DIFFRACTION43chain 'G' and (resid 178 through 264 )G178 - 264

+
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