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- PDB-5ik2: Caldalaklibacillus thermarum F1-ATPase (epsilon mutant) -

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Basic information

Entry
Database: PDB / ID: 5ik2
TitleCaldalaklibacillus thermarum F1-ATPase (epsilon mutant)
Components(ATP synthase ...) x 4
KeywordsHYDROLASE / F1-ATPase / Complex
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha
Similarity search - Component
Biological speciesCaldalkalibacillus thermarum TA2.A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFerguson, S.A. / Cook, G.M. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U1065663150 United Kingdom
Medical Research Council (United Kingdom)U105184325 United Kingdom
Medical Research Council (United Kingdom)MR/M009858/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum.
Authors: Ferguson, S.A. / Cook, G.M. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
I: ATP synthase subunit alpha
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit beta
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase gamma chain
P: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)715,80756
Polymers708,77416
Non-polymers7,03340
Water19,4561080
1
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,81227
Polymers354,3878
Non-polymers3,42419
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: ATP synthase subunit alpha
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit beta
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase gamma chain
P: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,99629
Polymers354,3878
Non-polymers3,60921
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.240, 131.290, 212.010
Angle α, β, γ (deg.)90.000, 108.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21I
12B
22J
13C
23K
14D
24L
15E
25M
16F
26N
17G
27O

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUVALVALAA27 - 414 - 18
211GLUGLUVALVALII27 - 414 - 18
121LYSLYSGLNGLNAA46 - 6423 - 41
221LYSLYSGLNGLNII46 - 6423 - 41
131ASNASNTHRTHRAA70 - 9147 - 68
231ASNASNTHRTHRII70 - 9147 - 68
141PROPROPROPROAA98 - 50075 - 477
241PROPROPROPROII98 - 50075 - 477
112VALVALGLUGLUBB26 - 683 - 45
212VALVALGLUGLUJJ26 - 683 - 45
122ASNASNASNASNBB70 - 10947 - 86
222ASNASNASNASNJJ70 - 10947 - 86
132LEULEUARGARGBB111 - 11888 - 95
232LEULEUARGARGJJ111 - 11888 - 95
142GLUGLUPROPROBB122 - 28099 - 257
242GLUGLUPROPROJJ122 - 28099 - 257
152GLYGLYARGARGBB282 - 383259 - 360
252GLYGLYARGARGJJ282 - 383259 - 360
162ASPASPASPASPBB385 - 446362 - 423
262ASPASPASPASPJJ385 - 446362 - 423
172VALVALILEILEBB450 - 475427 - 452
272VALVALILEILEJJ450 - 475427 - 452
182GLUGLUSERSERBB480 - 501457 - 478
282GLUGLUSERSERJJ480 - 501457 - 478
113VALVALGLYGLYCC142 - 160119 - 137
213VALVALGLYGLYKK142 - 160119 - 137
123ARGARGLYSLYSCC164 - 175141 - 152
223ARGARGLYSLYSKK164 - 175141 - 152
133PROPROPHEPHECC317 - 398294 - 375
233PROPROPHEPHEKK317 - 398294 - 375
143ASPASPALAALACC403 - 502380 - 479
243ASPASPALAALAKK403 - 502380 - 479
114ASNASNALAALADD2 - 752 - 75
214ASNASNALAALALL2 - 752 - 75
124SERSERLEULEUDD78 - 12178 - 121
224SERSERLEULEULL78 - 12178 - 121
134ILEILELEULEUDD127 - 462127 - 462
234ILEILELEULEULL127 - 462127 - 462
115VALVALASPASPEE13 - 9813 - 98
215VALVALASPASPMM13 - 9813 - 98
125PROPROPROPROEE110 - 116110 - 116
225PROPROPROPROMM110 - 116110 - 116
135ALAALAILEILEEE124 - 399124 - 399
235ALAALAILEILEMM124 - 399124 - 399
145ARGARGLEULEUEE401 - 462401 - 462
245ARGARGLEULEUMM401 - 462401 - 462
116ASNASNALAALAFF2 - 1052 - 105
216ASNASNALAALANN2 - 1052 - 105
126GLUGLUGLUGLUFF107 - 443107 - 443
226GLUGLUGLUGLUNN107 - 443107 - 443
136ALAALALEULEUFF445 - 462445 - 462
236ALAALALEULEUNN445 - 462445 - 462
117ALAALAILEILEGG30 - 10329 - 102
217ALAALAILEILEOO30 - 10329 - 102
127GLUGLUSERSERGG105 - 193104 - 192
227GLUGLUSERSEROO105 - 193104 - 192
137GLUGLUALAALAGG215 - 240214 - 239
237GLUGLUALAALAOO215 - 240214 - 239

NCS ensembles :
ID
1
2
3
4
5
6
7

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99996, 0.003934, -0.008087), (-0.008676, -0.658864, 0.752212), (-0.002369, 0.752251, 0.658872)-27.844049, 26.874029, -12.84852
3given(1), (1), (1)
4given(-0.999958, 0.009189, 0.000723), (-0.005484, -0.656223, 0.754547), (0.007408, 0.754511, 0.656246)-27.56459, 27.064939, -12.18318
5given(1), (1), (1)
6given(-0.99998, -0.003447, -0.005228), (-0.001702, -0.653803, 0.756663), (-0.006026, 0.756657, 0.653784)-27.197969, 27.292971, -12.77306
7given(1), (1), (1)
8given(-0.999842, 0.017677, 0.001659), (-0.010421, -0.659942, 0.751245), (0.014374, 0.751109, 0.660022)-27.1127, 26.773911, -11.92389
9given(1), (1), (1)
10given(-0.999977, -0.000522, -0.006785), (-0.004767, -0.657797, 0.75318), (-0.004856, 0.753195, 0.657779)-27.71627, 27.253389, -12.94302
11given(1), (1), (1)
12given(-0.99993, 0.004948, 0.01076), (0.004902, -0.6541, 0.756392), (0.010781, 0.756392, 0.65403)-26.73864, 27.481911, -12.20692
13given(1), (1), (1)
14given(-0.999892, 0.002969, 0.014382), (0.008825, -0.661287, 0.750081), (0.011738, 0.750127, 0.661189)-26.71966, 27.79764, -11.53839

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Components

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ATP synthase ... , 4 types, 16 molecules ABCIJKDEFLMNGOHP

#1: Protein
ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 52340.539 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: atpA, CathTA2_2809 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: F5LA74, H+-transporting two-sector ATPase
#2: Protein
ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 50266.012 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: atpD, CathTA2_2807 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: F5LA72, H+-transporting two-sector ATPase
#3: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 31801.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: atpG, CathTA2_2808 / Production host: Escherichia coli (E. coli) / References: UniProt: F5LA73
#4: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14766.154 Da / Num. of mol.: 2 / Mutation: D89A, R92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria)
Gene: atpC, CathTA2_2806 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: F5LA71

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Non-polymers , 5 types, 1120 molecules

#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1080 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.6
Details: PEG 4600, Bis-Tris, Tris-HCl, glycerol, MgCl2, ADP, NaCl
PH range: 6.6-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.6→201.4 Å / Num. obs: 220174 / % possible obs: 93.9 % / Redundancy: 1.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.641.60.273187.2
14.24-46.941.90.014185.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.1.27data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HKK

5hkk


Resolution: 2.6→201.4 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.529 / SU ML: 0.235 / SU R Cruickshank DPI: 1.862 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.862 / ESU R Free: 0.318
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 11066 5 %RANDOM
Rwork0.2126 ---
obs0.2138 209085 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.58 Å2 / Biso mean: 36.537 Å2 / Biso min: 4.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20.71 Å2
2---0.91 Å20 Å2
3---1.42 Å2
Refinement stepCycle: final / Resolution: 2.6→201.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49468 0 440 1111 51019
Biso mean--29.56 26.44 -
Num. residues----6445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01950734
X-RAY DIFFRACTIONr_bond_other_d0.0010.0249493
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.99168809
X-RAY DIFFRACTIONr_angle_other_deg0.8453113965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg556431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59224.3852228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.625158860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.30715379
X-RAY DIFFRACTIONr_chiral_restr0.0560.27867
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02157184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210767
X-RAY DIFFRACTIONr_mcbond_it0.63.65825772
X-RAY DIFFRACTIONr_mcbond_other0.63.65825771
X-RAY DIFFRACTIONr_mcangle_it1.1135.48132234
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A70095.54
2B69672.16
3C33131.54
4D69083.78
5E65551.21
6F69711.7
7G29692.86
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 756 -
Rwork0.298 14408 -
all-15164 -
obs--87.1 %

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