[English] 日本語
Yorodumi
- PDB-8bgb: Structure of the citrate-bound extracytoplasmic PAS domain of his... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bgb
TitleStructure of the citrate-bound extracytoplasmic PAS domain of histidine kinase CitA from Geobacillus thermodenitrificans
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / PAS domain / extracytoplasmic / citrate-bound / sensor histidine kinase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. ...SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
CITRATE ANION / Histidine kinase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBecker, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Structure of the citrate-bound extracytoplasmic PAS domain of histidine kinase CitA from Geobacillus thermodenitrificans
Authors: Becker, S.
History
DepositionOct 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Histidine kinase
BBB: Histidine kinase
CCC: Histidine kinase
DDD: Histidine kinase
EEE: Histidine kinase
FFF: Histidine kinase
GGG: Histidine kinase
HHH: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,54517
Polymers113,0098
Non-polymers1,5369
Water13,079726
1
AAA: Histidine kinase
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,3152
Polymers14,1261
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Histidine kinase
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,3152
Polymers14,1261
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Histidine kinase
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,3152
Polymers14,1261
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Histidine kinase
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,3152
Polymers14,1261
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
EEE: Histidine kinase
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,3152
Polymers14,1261
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
FFF: Histidine kinase
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,3152
Polymers14,1261
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
GGG: Histidine kinase
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,3383
Polymers14,1261
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
HHH: Histidine kinase
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,3152
Polymers14,1261
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.209, 101.140, 77.877
Angle α, β, γ (deg.)90.000, 105.626, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74AAA
84EEE
95AAA
105FFF
116AAA
126GGG
137AAA
147HHH
158BBB
168CCC
179BBB
189DDD
1910BBB
2010EEE
2111BBB
2211FFF
2312BBB
2412GGG
2513BBB
2613HHH
2714CCC
2814DDD
2915CCC
3015EEE
3116CCC
3216FFF
3317CCC
3417GGG
3518CCC
3618HHH
3719DDD
3819EEE
3920DDD
4020FFF
4121DDD
4221GGG
4322DDD
4422HHH
4523EEE
4623FFF
4724EEE
4824GGG
4925EEE
5025HHH
5126FFF
5226GGG
5327FFF
5427HHH
5528GGG
5628HHH

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERARGARGAAAA32 - 1602 - 130
211SERSERARGARGBBBB32 - 1602 - 130
322SERSERGLNGLNAAAA32 - 1592 - 129
422SERSERGLNGLNCCCC32 - 1592 - 129
533SERSERASPASPAAAA32 - 1572 - 127
633SERSERASPASPDDDD32 - 1572 - 127
744SERSERTHRTHRAAAA32 - 1612 - 131
844SERSERTHRTHREEEE32 - 1612 - 131
955SERSERASPASPAAAA32 - 1572 - 127
1055SERSERASPASPFFFF32 - 1572 - 127
1166THRTHRGLNGLNAAAA33 - 1593 - 129
1266THRTHRGLNGLNGGGG33 - 1593 - 129
1377SERSERILEILEAAAA32 - 1582 - 128
1477SERSERILEILEHHHH32 - 1582 - 128
1588SERSERARGARGBBBB32 - 1602 - 130
1688SERSERARGARGCCCC32 - 1602 - 130
1799SERSERILEILEBBBB32 - 1582 - 128
1899SERSERILEILEDDDD32 - 1582 - 128
191010SERSERARGARGBBBB32 - 1602 - 130
201010SERSERARGARGEEEE32 - 1602 - 130
211111SERSERILEILEBBBB32 - 1582 - 128
221111SERSERILEILEFFFF32 - 1582 - 128
231212THRTHRARGARGBBBB33 - 1603 - 130
241212THRTHRARGARGGGGG33 - 1603 - 130
251313SERSERGLNGLNBBBB32 - 1592 - 129
261313SERSERGLNGLNHHHH32 - 1592 - 129
271414SERSERASPASPCCCC32 - 1572 - 127
281414SERSERASPASPDDDD32 - 1572 - 127
291515SERSERGLNGLNCCCC32 - 1592 - 129
301515SERSERGLNGLNEEEE32 - 1592 - 129
311616SERSERASPASPCCCC32 - 1572 - 127
321616SERSERASPASPFFFF32 - 1572 - 127
331717THRTHRGLNGLNCCCC33 - 1593 - 129
341717THRTHRGLNGLNGGGG33 - 1593 - 129
351818SERSERILEILECCCC32 - 1582 - 128
361818SERSERILEILEHHHH32 - 1582 - 128
371919SERSERASPASPDDDD32 - 1572 - 127
381919SERSERASPASPEEEE32 - 1572 - 127
392020SERSERILEILEDDDD32 - 1582 - 128
402020SERSERILEILEFFFF32 - 1582 - 128
412121THRTHRASPASPDDDD33 - 1573 - 127
422121THRTHRASPASPGGGG33 - 1573 - 127
432222SERSERASPASPDDDD32 - 1572 - 127
442222SERSERASPASPHHHH32 - 1572 - 127
452323SERSERASPASPEEEE32 - 1572 - 127
462323SERSERASPASPFFFF32 - 1572 - 127
472424THRTHRGLNGLNEEEE33 - 1593 - 129
482424THRTHRGLNGLNGGGG33 - 1593 - 129
492525SERSERILEILEEEEE32 - 1582 - 128
502525SERSERILEILEHHHH32 - 1582 - 128
512626THRTHRASPASPFFFF33 - 1573 - 127
522626THRTHRASPASPGGGG33 - 1573 - 127
532727SERSERASPASPFFFF32 - 1572 - 127
542727SERSERASPASPHHHH32 - 1572 - 127
552828THRTHRILEILEGGGG33 - 1583 - 128
562828THRTHRILEILEHHHH33 - 1583 - 128

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

-
Components

#1: Protein
Histidine kinase /


Mass: 14126.153 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Strain: NG80-2 / Gene: GTNG_1840 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4IPE6, histidine kinase
#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 1 M tri-sodium citrate, pH 9.0, 0.1 M imidazole

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→48.79 Å / Num. obs: 105114 / % possible obs: 98.9 % / Redundancy: 6.85 % / Rrim(I) all: 0.0486 / Net I/σ(I): 16.47
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 3571 / Rrim(I) all: 0.295

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J80
Resolution: 1.7→48.79 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.17 / Average fsc free: 0.9329 / Average fsc work: 0.942 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1958 5202 4.956 %
Rwork0.1666 99771 -
all0.168 --
obs-104973 99.866 %
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: 24.204 Å2
Baniso -1Baniso -2Baniso -3
1-0.333 Å2-0 Å2-0.513 Å2
2--0.145 Å20 Å2
3----0.165 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 105 726 8466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138075
X-RAY DIFFRACTIONr_bond_other_d0.0350.0157913
X-RAY DIFFRACTIONr_angle_refined_deg1.651.63910923
X-RAY DIFFRACTIONr_angle_other_deg2.3431.57718162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25251068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.37520.762407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.369151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9441580
X-RAY DIFFRACTIONr_chiral_restr0.0850.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029354
X-RAY DIFFRACTIONr_gen_planes_other0.0210.021838
X-RAY DIFFRACTIONr_nbd_refined0.2160.21521
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.27406
X-RAY DIFFRACTIONr_nbtor_refined0.1580.24045
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.23958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2569
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1290.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.251
X-RAY DIFFRACTIONr_nbd_other0.2480.2219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.220.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0130.21
X-RAY DIFFRACTIONr_mcbond_it2.152.2824227
X-RAY DIFFRACTIONr_mcbond_other2.1512.2814226
X-RAY DIFFRACTIONr_mcangle_it2.8913.4095312
X-RAY DIFFRACTIONr_mcangle_other2.893.415313
X-RAY DIFFRACTIONr_scbond_it3.4532.7163848
X-RAY DIFFRACTIONr_scbond_other3.4542.7163847
X-RAY DIFFRACTIONr_scangle_it5.1743.9035611
X-RAY DIFFRACTIONr_scangle_other5.1733.9035612
X-RAY DIFFRACTIONr_lrange_it6.37328.7798885
X-RAY DIFFRACTIONr_lrange_other6.37328.7798886
X-RAY DIFFRACTIONr_ncsr_local_group_10.0920.053842
X-RAY DIFFRACTIONr_ncsr_local_group_20.1090.053840
X-RAY DIFFRACTIONr_ncsr_local_group_30.1130.053781
X-RAY DIFFRACTIONr_ncsr_local_group_40.0840.054006
X-RAY DIFFRACTIONr_ncsr_local_group_50.1020.053787
X-RAY DIFFRACTIONr_ncsr_local_group_60.0780.053952
X-RAY DIFFRACTIONr_ncsr_local_group_70.0970.053829
X-RAY DIFFRACTIONr_ncsr_local_group_80.1110.053699
X-RAY DIFFRACTIONr_ncsr_local_group_90.1040.053669
X-RAY DIFFRACTIONr_ncsr_local_group_100.0710.053800
X-RAY DIFFRACTIONr_ncsr_local_group_110.0980.053678
X-RAY DIFFRACTIONr_ncsr_local_group_120.0820.053791
X-RAY DIFFRACTIONr_ncsr_local_group_130.0980.053707
X-RAY DIFFRACTIONr_ncsr_local_group_140.0750.054034
X-RAY DIFFRACTIONr_ncsr_local_group_150.10.053953
X-RAY DIFFRACTIONr_ncsr_local_group_160.0690.054037
X-RAY DIFFRACTIONr_ncsr_local_group_170.0960.053947
X-RAY DIFFRACTIONr_ncsr_local_group_180.0660.054089
X-RAY DIFFRACTIONr_ncsr_local_group_190.0970.053784
X-RAY DIFFRACTIONr_ncsr_local_group_200.080.053880
X-RAY DIFFRACTIONr_ncsr_local_group_210.1050.053754
X-RAY DIFFRACTIONr_ncsr_local_group_220.0690.053915
X-RAY DIFFRACTIONr_ncsr_local_group_230.0860.053736
X-RAY DIFFRACTIONr_ncsr_local_group_240.0690.053848
X-RAY DIFFRACTIONr_ncsr_local_group_250.0840.053787
X-RAY DIFFRACTIONr_ncsr_local_group_260.0950.053778
X-RAY DIFFRACTIONr_ncsr_local_group_270.0510.053930
X-RAY DIFFRACTIONr_ncsr_local_group_280.0950.053889
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.091910.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.091910.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.109130.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.109130.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.11330.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.11330.05009
47AAAX-RAY DIFFRACTIONLocal ncs0.083820.0501
48EEEX-RAY DIFFRACTIONLocal ncs0.083820.0501
59AAAX-RAY DIFFRACTIONLocal ncs0.102020.05009
510FFFX-RAY DIFFRACTIONLocal ncs0.102020.05009
611AAAX-RAY DIFFRACTIONLocal ncs0.077560.0501
612GGGX-RAY DIFFRACTIONLocal ncs0.077560.0501
713AAAX-RAY DIFFRACTIONLocal ncs0.096980.05008
714HHHX-RAY DIFFRACTIONLocal ncs0.096980.05008
815BBBX-RAY DIFFRACTIONLocal ncs0.110510.05009
816CCCX-RAY DIFFRACTIONLocal ncs0.110510.05009
917BBBX-RAY DIFFRACTIONLocal ncs0.103570.05009
918DDDX-RAY DIFFRACTIONLocal ncs0.103570.05009
1019BBBX-RAY DIFFRACTIONLocal ncs0.071380.0501
1020EEEX-RAY DIFFRACTIONLocal ncs0.071380.0501
1121BBBX-RAY DIFFRACTIONLocal ncs0.098060.05009
1122FFFX-RAY DIFFRACTIONLocal ncs0.098060.05009
1223BBBX-RAY DIFFRACTIONLocal ncs0.08220.0501
1224GGGX-RAY DIFFRACTIONLocal ncs0.08220.0501
1325BBBX-RAY DIFFRACTIONLocal ncs0.09830.05009
1326HHHX-RAY DIFFRACTIONLocal ncs0.09830.05009
1427CCCX-RAY DIFFRACTIONLocal ncs0.074530.05009
1428DDDX-RAY DIFFRACTIONLocal ncs0.074530.05009
1529CCCX-RAY DIFFRACTIONLocal ncs0.099840.05009
1530EEEX-RAY DIFFRACTIONLocal ncs0.099840.05009
1631CCCX-RAY DIFFRACTIONLocal ncs0.069410.05009
1632FFFX-RAY DIFFRACTIONLocal ncs0.069410.05009
1733CCCX-RAY DIFFRACTIONLocal ncs0.096120.05009
1734GGGX-RAY DIFFRACTIONLocal ncs0.096120.05009
1835CCCX-RAY DIFFRACTIONLocal ncs0.06610.05009
1836HHHX-RAY DIFFRACTIONLocal ncs0.06610.05009
1937DDDX-RAY DIFFRACTIONLocal ncs0.097230.05009
1938EEEX-RAY DIFFRACTIONLocal ncs0.097230.05009
2039DDDX-RAY DIFFRACTIONLocal ncs0.079630.05009
2040FFFX-RAY DIFFRACTIONLocal ncs0.079630.05009
2141DDDX-RAY DIFFRACTIONLocal ncs0.104510.05009
2142GGGX-RAY DIFFRACTIONLocal ncs0.104510.05009
2243DDDX-RAY DIFFRACTIONLocal ncs0.068770.05009
2244HHHX-RAY DIFFRACTIONLocal ncs0.068770.05009
2345EEEX-RAY DIFFRACTIONLocal ncs0.08570.05009
2346FFFX-RAY DIFFRACTIONLocal ncs0.08570.05009
2447EEEX-RAY DIFFRACTIONLocal ncs0.068670.0501
2448GGGX-RAY DIFFRACTIONLocal ncs0.068670.0501
2549EEEX-RAY DIFFRACTIONLocal ncs0.084240.05009
2550HHHX-RAY DIFFRACTIONLocal ncs0.084240.05009
2651FFFX-RAY DIFFRACTIONLocal ncs0.094740.05009
2652GGGX-RAY DIFFRACTIONLocal ncs0.094740.05009
2753FFFX-RAY DIFFRACTIONLocal ncs0.050950.05009
2754HHHX-RAY DIFFRACTIONLocal ncs0.050950.05009
2855GGGX-RAY DIFFRACTIONLocal ncs0.095260.05009
2856HHHX-RAY DIFFRACTIONLocal ncs0.095260.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3073820.2577332X-RAY DIFFRACTION99.4841
1.744-1.7920.2513620.2427142X-RAY DIFFRACTION99.8005
1.792-1.8440.2943280.2147039X-RAY DIFFRACTION99.7292
1.844-1.9010.2363500.2046791X-RAY DIFFRACTION99.8881
1.901-1.9630.2373550.1886509X-RAY DIFFRACTION99.8981
1.963-2.0320.2153370.1826333X-RAY DIFFRACTION99.985
2.032-2.1080.2083630.1776101X-RAY DIFFRACTION99.7377
2.108-2.1940.2063100.1675879X-RAY DIFFRACTION99.71
2.194-2.2920.1773030.1665705X-RAY DIFFRACTION99.9667
2.292-2.4040.2132910.1655383X-RAY DIFFRACTION100
2.404-2.5330.2052800.165163X-RAY DIFFRACTION99.9816
2.533-2.6870.22520.1634876X-RAY DIFFRACTION99.9805
2.687-2.8720.1932430.1554598X-RAY DIFFRACTION100
2.872-3.1020.1772040.1534292X-RAY DIFFRACTION99.9778
3.102-3.3970.1831830.1593973X-RAY DIFFRACTION100
3.397-3.7970.1661960.1513566X-RAY DIFFRACTION100
3.797-4.3830.1631590.1353141X-RAY DIFFRACTION99.9092
4.383-5.3630.1721430.1482683X-RAY DIFFRACTION100
5.363-7.5660.2131040.1932085X-RAY DIFFRACTION100

+
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