[English] 日本語
Yorodumi
- PDB-6s5n: Non-square conformations of KtrA E125Q mutant rings with bound ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s5n
TitleNon-square conformations of KtrA E125Q mutant rings with bound ATP
ComponentsKtr system potassium uptake protein A
KeywordsTRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / non-square conformation octameric ring / atp
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
: / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.09 Å
AuthorsTeixeira-Duarte, C.M. / Fonseca, F. / Morais-Cabral, J.H.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/29863/2017 Portugal
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-007274 Portugal
CitationJournal: Elife / Year: 2019
Title: Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site.
Authors: Teixeira-Duarte, C.M. / Fonseca, F. / Morais Cabral, J.H.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,38416
Polymers199,3268
Non-polymers4,0578
Water00
1
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
hetero molecules

G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,38416
Polymers199,3268
Non-polymers4,0578
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555x+1/2,y+1/2,z1
crystal symmetry operation8_545x+1/2,-y-1/2,-z1
2
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
hetero molecules

C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,38416
Polymers199,3268
Non-polymers4,0578
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Unit cell
Length a, b, c (Å)109.111, 156.535, 286.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain G
21chain H
31chain A
41chain B
51chain C
61chain D
71chain E
81chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNchain GGG6 - 1406 - 140
2ASNASNchain HHH6 - 1406 - 140
3METMETchain AAA6 - 2226 - 222
4METMETchain BBB6 - 2226 - 222
5METMETchain CCC6 - 2226 - 222
6METMETchain DDD6 - 2226 - 222
7METMETchain EEE6 - 2226 - 222
8METMETchain FFF6 - 2226 - 222

-
Components

#1: Protein
Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


Mass: 24915.775 Da / Num. of mol.: 8 / Mutation: E125Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 100mM MES pH 6.5, 6% PEG 4000, 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 4.09→48.24 Å / Num. obs: 19704 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.053 / Rrim(I) all: 0.137 / Net I/σ(I): 9.5
Reflection shellResolution: 4.09→4.48 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.135 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4578 / CC1/2: 0.835 / Rpim(I) all: 0.467 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4j90
Resolution: 4.09→48.24 Å / SU ML: 0.89 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 41.22
RfactorNum. reflection% reflection
Rfree0.3199 3789 10.22 %
Rwork0.2791 --
obs0.2833 19704 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 335.88 Å2 / Biso min: 59.15 Å2
Refinement stepCycle: final / Resolution: 4.09→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12346 0 248 0 12594
Biso mean--178.97 --
Num. residues----1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312800
X-RAY DIFFRACTIONf_angle_d0.80417350
X-RAY DIFFRACTIONf_chiral_restr0.0322000
X-RAY DIFFRACTIONf_plane_restr0.0032174
X-RAY DIFFRACTIONf_dihedral_angle_d16.6854768
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11G7658X-RAY DIFFRACTION3.482TORSIONAL
12H7658X-RAY DIFFRACTION3.482TORSIONAL
13A7658X-RAY DIFFRACTION3.482TORSIONAL
14B7658X-RAY DIFFRACTION3.482TORSIONAL
15C7658X-RAY DIFFRACTION3.482TORSIONAL
16D7658X-RAY DIFFRACTION3.482TORSIONAL
17E7658X-RAY DIFFRACTION3.482TORSIONAL
18F7658X-RAY DIFFRACTION3.482TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.09-4.14560.61941130.4177115089
4.1456-4.20010.44081310.40861215100
4.2001-4.25760.42671430.3551219100
4.2576-4.31840.41671460.3581276100
4.3184-4.38280.33471350.35851225100
4.3828-4.45130.35881320.35571215100
4.4513-4.52420.41191380.3439129299
4.5242-4.60210.38711100.3377121599
4.6021-4.68570.35931420.3419121099
4.6857-4.77580.31591540.32331318100
4.7758-4.87320.40221300.34791189100
4.8732-4.9790.42291290.35531269100
4.979-5.09470.40581740.36031166100
5.0947-5.2220.45511460.34461249100
5.222-5.3630.41951470.32891245100
5.363-5.52060.41521480.31671214100
5.5206-5.69850.39091880.33531206100
5.6985-5.90190.44511630.3491215100
5.9019-6.13770.38421320.33061243100
6.1377-6.41650.3321330.32321266100
6.4165-6.75390.43381440.30511240100
6.7539-7.17580.35931310.2851238100
7.1758-7.72770.30111240.26931242100
7.7277-8.50160.27131340.21631255100
8.5016-9.72310.19741510.18331228100
9.7231-12.2170.17931750.1879121199
12.217-48.240.3378960.2509127399
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)
16.608-0.39421.61066.90142.42522.01180.5021-0.0657-0.61550.04310.537-0.67130.50561.2664-0.42191.5521-0.532-1.07741.6535-0.00330.160919.69171.4328-29.7795
23.88540.7594-4.68242.0667-0.82989.6138-0.7441-0.0644-0.20181.1811-1.065-0.16190.6979-0.39750.95261.7803-0.87080.17040.8886-1.21291.720122.08850.4578-21.986
33.2737-0.7972-1.05345.4762.28422.5456-1.0402-0.8984-0.59050.88811.5839-2.1743-0.0980.5066-0.26852.0754-0.0694-0.75460.83920.10691.171321.02598.6544-21.4148
41.8417-1.81570.82275.06412.93164.6271-0.2880.3939-0.2169-0.57930.5949-0.36440.2087-0.11210.04922.5122-0.0398-0.09390.199-0.21670.955111.630214.3149-24.1098
52.2282-1.6142-0.14077.74170.46770.04150.57280.4118-0.89611.09910.55080.035-0.1891-0.7565-0.83532.39040.0331-0.25282.24-0.24190.44763.404613.7815-28.5274
61.6125-2.3681-1.93894.87180.05487.85720.8709-0.2924-0.3110.1767-0.34060.66110.7345-0.9726-0.18532.8399-0.912-0.71912.96242.5691-0.4783-1.4225-4.1573-36.502
77.46270.9294-1.0591.98766.06072.0290.39760.55191.40890.4729-0.30820.8563-1.2264-0.5788-0.2212.5713-0.1656-0.45591.01330.19321.2474-0.4206-5.0609-49.3506
86.73021.6157-1.28459.6425-1.70785.6970.3434-0.0435-0.6595-0.1846-2.5588-1.30010.3499-0.4911.14782.2898-0.6405-0.48041.4093-0.00260.86183.0469-14.9746-60.1585
91.8482-1.39732.99631.4523-1.71275.58690.03790.2021-0.2549-0.7253-0.4041-0.01680.6774-0.91130.07812.8992-0.6861-0.53062.28240.93961.62067.2117-18.3524-60.543
102.0214.8046-2.39869.9315-1.65444.8780.5151-0.39290.88690.0230.17260.30010.4727-0.0698-0.38982.1765-1.2233-0.22491.39350.39921.3904-4.5752-8.5112-55.7409
112.8386-1.79910.96162.5557-0.94892.49170.3598-0.9330.60790.41460.36452.08750.7863-1.9992-0.59661.4902-0.97820.19731.76910.06351.6447-10.5526-11.3737-27.6339
121.98132.0412-1.6042.1976-1.70643.480.66220.008-0.0071-0.21130.113-0.22271.52180.651-0.58571.5208-0.4659-0.09411.25560.59250.915112.57311.6134-48.5219
131.9786-2.80413.25646.1614-5.6375.248-1.4143-0.8308-0.88660.6529-0.6247-1.24730.277-0.5221.33410.84920.0562-0.26412.3785-0.32771.6376-48.911623.4756-47.9324
141.245-2.5719-1.02347.05871.48250.91640.0602-1.9131.12661.2146-0.01940.20430.157-0.3945-0.08661.8518-0.2794-0.16011.8687-0.46411.7023-53.932817.0979-49.3108
150.38470.8624-0.03963.19482.76847.3675-1.37320.8438-0.1147-0.8348-0.83740.42530.2231-1.70721.34071.6715-0.73430.10262.6310.09121.8729-59.714118.8558-53.5217
167.51560.71180.02745.39962.20129.9064-0.53540.42060.3818-0.05330.34012.25610.6137-0.62260.11960.89581.1303-1.0161.2769-0.40191.8401-55.188627.0893-55.9562
170.3587-1.62220.29971.9853.06282.62080.1111-0.66460.71720.82580.6672-0.2401-0.03270.0489-0.22141.77321.4683-2.682.3181-1.93770.2779-55.69226.1333-65.7775
186.2939-3.49293.30451.99041.17253.83660.46160.8108-0.4906-1.2152-1.13250.199-0.5437-0.87910.2382.08132.0733-0.31021.14590.49481.5102-50.63529.8181-60.1674
197.39710.8168-4.33883.35641.9734.3940.5607-0.0427-0.70250.1792-0.73691.2432-0.06760.59580.12691.6488-0.19370.16972.5271-0.01211.5633-45.106130.838-66.6535
201.27992.1270.0781.9730.76192.83360.16210.85470.6361.61150.4777-0.06130.2747-0.145-0.2271.6680.26220.13141.2942-0.0241.0105-24.791729.8963-53.1605
211.4934-2.1456-1.80243.10022.65512.226-0.2843-0.0049-0.2654-0.0004-0.301-0.3801-0.14240.37750.14371.69720.226-1.30881.4199-3.09310.8116-7.172533.3238-39.8598
229.0434-2.9165-2.59283.5231.50855.7716-1.1577-0.28131.26561.8293-0.4432-1.0748-0.1151-0.62851.08181.297-0.3293-0.24931.8188-0.3031.115-16.879336.2325-38.7894
232.84572.67940.20635.8252-2.2261.8102-0.4094-0.58330.67151.0478-0.0634-2.3442-0.12191.20640.27271.77820.1421-0.66671.9017-0.14071.3469-12.964932.9619-34.2742
246.98323.5908-6.90172.0295-3.13132.01060.68060.11050.2056-0.20971.1944-0.2075-0.84691.0068-0.98890.9909-0.24510.04092.6621-0.31610.9193-14.777136.3848-49.9288
252.20080.3565-0.02275.1741-0.70494.850.67880.4-0.2771-0.5686-0.07760.40940.29370.1716-0.40120.89690.07620.25010.4081-0.00141.1081-24.719811.4107-61.2182
262.1035-1.1107-0.60643.4117-1.14952.5981.0840.25320.57451.8897-0.66562.5523-2.0317-0.4354-0.01731.97620.25560.6581.1117-0.0181.6313-35.963542.2115-42.0703
272.8416-0.29780.29180.87770.43990.76560.6023-0.97840.35950.40220.0782.10530.5667-0.6468-0.38160.4299-0.17930.35561.8905-0.70222.0692-50.0136-13.9559-41.7382
284.4402-4.09322.45168.4154-4.01032.0469-0.0415-0.99010.4327-0.1472-0.03770.5244-0.44-0.6548-0.09221.2503-0.23290.3871.0779-0.31031.622-42.2816-9.6337-39.642
293.9971.44290.30817.03960.49413.2067-0.304-0.7179-1.1263-0.3765-0.6882-0.7904-0.2816-0.18860.55261.5616-0.5626-0.28390.86280.18011.1529-34.5228-7.0239-46.0617
301.0177-1.8411.3042.7941-2.09081.5220.18240.2861-0.12160.8315-0.0328-0.6859-0.566-1.07290.06121.1136-0.6599-0.00881.06960.06761.2624-28.9323-32.2396-55.5855
310.7169-0.8-1.87171.11912.21465.0230.6424-0.4449-0.68950.5666-0.8677-0.4925-0.12060.46820.37150.78610.0388-0.33571.12730.40991.3091-28.2275-50.9999-52.5679
326.1290.1724-0.01991.69550.13852.8332-0.34030.2578-1.7582-0.39130.0677-1.4418-0.09431.52040.22460.7973-0.04190.36571.42930.16810.8999-26.0007-46.9064-54.2994
335.02353.92692.99044.317-0.31627.48660.04660.2620.72790.4718-0.82490.1383-0.6191.64340.38712.15970.28080.28170.64370.98430.8863-29.8024-23.8769-67.4463
343.99190.466-0.72928.2253-2.27576.1092-0.51480.05190.4943-0.0356-0.3401-0.1308-0.7340.20950.67322.1708-0.2408-0.22630.88970.1951.1683-30.3374-17.5156-72.6809
353.59431.30530.51233.6157-0.7063.7972-0.70751.26561.343-1.15630.410.7123-0.46780.80670.15151.01020.0569-0.37131.50190.29491.0041-35.7502-22.2872-76.7277
362.79561.2794-0.70983.096-0.95544.08720.0863-1.1576-0.4303-0.3696-0.86910.1515-0.7893-1.01630.46540.2643-0.0771-0.20851.1510.26121.2407-46.7252-28.1598-68.8741
378.04-3.52681.28942.0082-3.65686.66780.337-0.74810.16511.8313-0.8117-1.3962-0.3374-1.44690.42411.2968-0.3092-0.20731.4517-0.18910.9999-36.9035-29.3868-43.2198
382.9873-2.2183-1.20942.2273.15889.8529-0.3112-0.3245-0.03952.0577-0.8819-0.6760.90360.23761.3511.9661-0.5437-0.26421.13780.33751.0996-23.736-36.7-31.1965
39-0.0051-0.01340.0097-0.00280.00270.00350.5003-1.6742-0.26791.00530.1628-1.13810.48251.0332-0.63482.00380.1316-1.10151.896-0.00971.9277-18.5659-35.5467-31.5083
405.5767-1.303-4.0981.7976-0.75674.82780.6229-1.281-0.16130.5286-0.49270.3309-1.02160.2354-0.30132.4208-0.3965-0.62142.8389-0.56271.4378-34.5567-36.0339-32.7735
410.411-0.52590.45121.14591.04285.6454-0.3071.17430.4751-0.4335-0.2771-0.215-0.6068-0.42770.23361.349-0.5191-1.13211.5337-0.58952.2989-38.8946-41.6372.9614
424.25193.8701-0.26552.00984.6346.7405-0.26740.70570.1446-0.5999-0.9050.6110.1526-0.44050.64040.91-0.831-0.12693.0219-0.53291.5804-32.5223-47.27092.4168
433.01031.8784-0.10513.7710.77285.0949-0.4136-0.2858-0.13360.58820.4688-1.641-0.66690.4146-0.1081.27140.2277-0.39391.2601-0.19351.0529-40.9719-49.21215.1746
447.5129-2.5307-8.04352.0125-7.94592.036-0.58660.6553-0.1465-0.6062-0.22991.51360.3945-1.30530.21942.96860.7636-2.18590.08981.35220.2199-55.0699-49.704816.1446
452.67231.799-0.32023.37590.14180.09651.3014-0.3293-0.26580.39520.13090.32950.2489-0.8434-1.00523.1041.14890.40661.78540.49731.2978-59.0486-41.5727-2.7413
466.6765-3.96171.12264.7227-2.42641.9728-0.2854-1.58820.45640.43140.39261.3649-0.4244-0.2211-0.21190.7616-0.1192-0.51582.68230.05551.9794-67.6803-47.334-5.9751
474.87220.7685-0.18651.7008-2.79884.983-0.51370.2589-0.1247-0.68760.08910.59520.3503-0.43480.3011.7772-1.1989-0.06382.41780.11481.707-70.871-57.276-7.5442
481.58620.6261-1.29943.74190.65811.548-0.20120.03710.14970.1219-0.6550.5306-0.8227-1.6290.47541.2698-0.7813-1.77653.1538-0.558-0.4256-62.5599-55.6972-16.6172
492.7839-1.5994-2.04692.6237-0.41863.03721.2281-0.49320.5445-0.71140.2653-0.0188-0.5521-0.345-0.71563.38430.3145-0.4751.7140.00480.0929-54.2005-50.9364-16.7304
504.3913-1.8561-5.27298.37064.11686.72612.14830.2114-1.10370.59682.16680.4081-0.45030.3373-2.41712.7813-0.0482-1.00410.9923-0.17611.6705-46.9785-37.85381.3123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 27 )A6 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 44 )A28 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 81 )A45 - 81
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 106 )A82 - 106
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 123 )A107 - 123
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 137 )A124 - 137
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 157 )A138 - 157
8X-RAY DIFFRACTION8chain 'A' and (resid 158 through 191 )A158 - 191
9X-RAY DIFFRACTION9chain 'A' and (resid 192 through 203 )A192 - 203
10X-RAY DIFFRACTION10chain 'A' and (resid 204 through 222 )A204 - 222
11X-RAY DIFFRACTION11chain 'B' and (resid 6 through 106 )B6 - 106
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 222 )B107 - 222
13X-RAY DIFFRACTION13chain 'C' and (resid 6 through 27 )C6 - 27
14X-RAY DIFFRACTION14chain 'C' and (resid 28 through 44 )C28 - 44
15X-RAY DIFFRACTION15chain 'C' and (resid 45 through 66 )C45 - 66
16X-RAY DIFFRACTION16chain 'C' and (resid 67 through 81 )C67 - 81
17X-RAY DIFFRACTION17chain 'C' and (resid 82 through 94 )C82 - 94
18X-RAY DIFFRACTION18chain 'C' and (resid 95 through 106 )C95 - 106
19X-RAY DIFFRACTION19chain 'C' and (resid 107 through 123 )C107 - 123
20X-RAY DIFFRACTION20chain 'C' and (resid 124 through 157 )C124 - 157
21X-RAY DIFFRACTION21chain 'C' and (resid 158 through 171 )C158 - 171
22X-RAY DIFFRACTION22chain 'C' and (resid 172 through 191 )C172 - 191
23X-RAY DIFFRACTION23chain 'C' and (resid 192 through 203 )C192 - 203
24X-RAY DIFFRACTION24chain 'C' and (resid 204 through 222 )C204 - 222
25X-RAY DIFFRACTION25chain 'D' and (resid 6 through 123 )D6 - 123
26X-RAY DIFFRACTION26chain 'D' and (resid 124 through 222 )D124 - 222
27X-RAY DIFFRACTION27chain 'E' and (resid 6 through 66 )E6 - 66
28X-RAY DIFFRACTION28chain 'E' and (resid 67 through 81 )E67 - 81
29X-RAY DIFFRACTION29chain 'E' and (resid 82 through 123 )E82 - 123
30X-RAY DIFFRACTION30chain 'E' and (resid 124 through 157 )E124 - 157
31X-RAY DIFFRACTION31chain 'E' and (resid 158 through 191 )E158 - 191
32X-RAY DIFFRACTION32chain 'E' and (resid 192 through 222 )E192 - 222
33X-RAY DIFFRACTION33chain 'F' and (resid 6 through 27 )F6 - 27
34X-RAY DIFFRACTION34chain 'F' and (resid 28 through 44 )F28 - 44
35X-RAY DIFFRACTION35chain 'F' and (resid 45 through 81 )F45 - 81
36X-RAY DIFFRACTION36chain 'F' and (resid 82 through 123 )F82 - 123
37X-RAY DIFFRACTION37chain 'F' and (resid 124 through 157 )F124 - 157
38X-RAY DIFFRACTION38chain 'F' and (resid 158 through 191 )F158 - 191
39X-RAY DIFFRACTION39chain 'F' and (resid 192 through 203 )F192 - 203
40X-RAY DIFFRACTION40chain 'F' and (resid 204 through 222 )F204 - 222
41X-RAY DIFFRACTION41chain 'G' and (resid 6 through 27 )G6 - 27
42X-RAY DIFFRACTION42chain 'G' and (resid 28 through 54 )G28 - 54
43X-RAY DIFFRACTION43chain 'G' and (resid 55 through 106 )G55 - 106
44X-RAY DIFFRACTION44chain 'G' and (resid 107 through 119 )G107 - 119
45X-RAY DIFFRACTION45chain 'G' and (resid 120 through 140 )G120 - 140
46X-RAY DIFFRACTION46chain 'H' and (resid 6 through 27 )H6 - 27
47X-RAY DIFFRACTION47chain 'H' and (resid 28 through 66 )H28 - 66
48X-RAY DIFFRACTION48chain 'H' and (resid 67 through 94 )H67 - 94
49X-RAY DIFFRACTION49chain 'H' and (resid 95 through 123 )H95 - 123
50X-RAY DIFFRACTION50chain 'H' and (resid 124 through 140 )H124 - 140

+
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