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- PDB-6foc: F1-ATPase from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 6foc
TitleF1-ATPase from Mycobacterium smegmatis
Components(ATP synthase ...) x 4
KeywordsHYDROLASE / Complex / Mycobacteria
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 hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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 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. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / 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 speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Mycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4 Å
AuthorsZhang, T. / Montgomery, M.G. / Leslie, A.G.W. / Cook, G.M. / Walker, J.E.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105663150 United Kingdom
Medical Research Council (United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (United Kingdom)MC_U105184325 United Kingdom
European Union201924 EDICT United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: The structure of the catalytic domain of the ATP synthase fromMycobacterium smegmatisis a target for developing antitubercular drugs.
Authors: Zhang, A.T. / Montgomery, M.G. / Leslie, A.G.W. / Cook, G.M. / Walker, J.E.
History
DepositionFeb 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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,ATP synthase subunit alpha,ATP synthase subunit alpha
B: ATP synthase subunit alpha,ATP synthase subunit alpha,ATP synthase subunit alpha
C: ATP synthase subunit alpha,ATP synthase subunit alpha,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)380,69319
Polymers378,3418
Non-polymers2,35311
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39190 Å2
ΔGint-227 kcal/mol
Surface area111500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.189, 105.189, 628.624
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C
14D
24E
15D
25F
16E
26F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEGLYGLYAA31 - 51031 - 510
21ILEILEGLYGLYBB31 - 51031 - 510
12ILEILEGLYGLYAA31 - 51031 - 510
22ILEILEGLYGLYCC31 - 51031 - 510
13GLUGLUPHEPHEBB30 - 51130 - 511
23GLUGLUPHEPHECC30 - 51130 - 511
14ALAALALEULEUDD9 - 4719 - 471
24ALAALALEULEUEE9 - 4719 - 471
15ALAALALEULEUDD9 - 4719 - 471
25ALAALALEULEUFF9 - 4719 - 471
16ALAALALEULEUEE9 - 4719 - 471
26ALAALALEULEUFF9 - 4719 - 471

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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ATP synthase ... , 4 types, 8 molecules ABCDEFGH

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


Mass: 58870.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: We are uncertain as to the register after residue 511 and so have built as UNK and numbered 1001-1011. These 11 residues are probably 512-522 but the resolution is not succinctly good to be ...Details: We are uncertain as to the register after residue 511 and so have built as UNK and numbered 1001-1011. These 11 residues are probably 512-522 but the resolution is not succinctly good to be certain. The complete sequence is MAELTISAADIEGAIEDYVSSFSADTEREEIGTVIDAGDGIAHVEGLPSVMTQELLEFPG GVLGVALNLDEHSVGAVILGEFEKIEEGQQVKRTGEVLSVPVGDAFLGRVVNPLGQPIDG QGDIAAETRRALELQAPSVVQRQSVSEPLQTGIKAIDAMTPIGRGQRQLIIGDRKTGKTA VCVDTILNQREAWLTGDPKQQVRCVYVAIGQKGTTIASVKRALEEGGAMEYTTIVAAPAS DAAGFKWLAPYTGSAIGQHWMYNGKHVLIVFDDLSKQADAYRAISLLLRRPPGREAFPGD VFYLHSRLLERCAKLSDELGGGSMTGLPIIETKANDISAFIPTNVISITDGQCFLESDLF NQGVRPAINVGVSVSRVGGAAQIKAMKEVAGSLRLDLSQYRELEAFAAFASDLDAASKAQ LDRGARLVELLKQPQYSPLAVEEQVVAIFLGTQGHLDSVPVEDVQRFESELLEHVKASHS DIFDGIRETKKLSEEAEEKLVSVINEFKKGFQASDGSSVVVSENAEALDPEDLEKESVKV RKPAPKKA,We are uncertain as to the register after residue 511 and so have built as UNK and numbered 1001-1011. These 11 residues are probably 512-522 but the resolution is not succinctly good to be certain. The complete sequence is MAELTISAADIEGAIEDYVSSFSADTEREEIGTVIDAGDGIAHVEGLPSVMTQELLEFPG GVLGVALNLDEHSVGAVILGEFEKIEEGQQVKRTGEVLSVPVGDAFLGRVVNPLGQPIDG QGDIAAETRRALELQAPSVVQRQSVSEPLQTGIKAIDAMTPIGRGQRQLIIGDRKTGKTA VCVDTILNQREAWLTGDPKQQVRCVYVAIGQKGTTIASVKRALEEGGAMEYTTIVAAPAS DAAGFKWLAPYTGSAIGQHWMYNGKHVLIVFDDLSKQADAYRAISLLLRRPPGREAFPGD VFYLHSRLLERCAKLSDELGGGSMTGLPIIETKANDISAFIPTNVISITDGQCFLESDLF NQGVRPAINVGVSVSRVGGAAQIKAMKEVAGSLRLDLSQYRELEAFAAFASDLDAASKAQ LDRGARLVELLKQPQYSPLAVEEQVVAIFLGTQGHLDSVPVEDVQRFESELLEHVKASHS DIFDGIRETKKLSEEAEEKLVSVINEFKKGFQASDGSSVVVSENAEALDPEDLEKESVKV RKPAPKKA,We are uncertain as to the register after residue 511 and so have built as UNK and numbered 1001-1011. These 11 residues are probably 512-522 but the resolution is not succinctly good to be certain. The complete sequence is MAELTISAADIEGAIEDYVSSFSADTEREEIGTVIDAGDGIAHVEGLPSVMTQELLEFPG GVLGVALNLDEHSVGAVILGEFEKIEEGQQVKRTGEVLSVPVGDAFLGRVVNPLGQPIDG QGDIAAETRRALELQAPSVVQRQSVSEPLQTGIKAIDAMTPIGRGQRQLIIGDRKTGKTA VCVDTILNQREAWLTGDPKQQVRCVYVAIGQKGTTIASVKRALEEGGAMEYTTIVAAPAS DAAGFKWLAPYTGSAIGQHWMYNGKHVLIVFDDLSKQADAYRAISLLLRRPPGREAFPGD VFYLHSRLLERCAKLSDELGGGSMTGLPIIETKANDISAFIPTNVISITDGQCFLESDLF NQGVRPAINVGVSVSRVGGAAQIKAMKEVAGSLRLDLSQYRELEAFAAFASDLDAASKAQ LDRGARLVELLKQPQYSPLAVEEQVVAIFLGTQGHLDSVPVEDVQRFESELLEHVKASHS DIFDGIRETKKLSEEAEEKLVSVINEFKKGFQASDGSSVVVSENAEALDPEDLEKESVKV RKPAPKKA,We are uncertain as to the register after residue 511 and so have built as UNK and numbered 1512-1522. These 11 residues are probably 512-522 but the resolution is not succinctly good to be certain. The complete sequence is MAELTISAADIEGAIEDYVSSFSADTEREEIGTVIDAGDGIAHVEGLPSVMTQELLEFPG GVLGVALNLDEHSVGAVILGEFEKIEEGQQVKRTGEVLSVPVGDAFLGRVVNPLGQPIDG QGDIAAETRRALELQAPSVVQRQSVSEPLQTGIKAIDAMTPIGRGQRQLIIGDRKTGKTA VCVDTILNQREAWLTGDPKQQVRCVYVAIGQKGTTIASVKRALEEGGAMEYTTIVAAPAS DAAGFKWLAPYTGSAIGQHWMYNGKHVLIVFDDLSKQADAYRAISLLLRRPPGREAFPGD VFYLHSRLLERCAKLSDELGGGSMTGLPIIETKANDISAFIPTNVISITDGQCFLESDLF NQGVRPAINVGVSVSRVGGAAQIKAMKEVAGSLRLDLSQYRELEAFAAFASDLDAASKAQ LDRGARLVELLKQPQYSPLAVEEQVVAIFLGTQGHLDSVPVEDVQRFESELLEHVKASHS DIFDGIRETKKLSEEAEEKLVSVINEFKKGFQASDGSSVVVSENAEALDPEDLEKESVKV RKPAPKKA
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria), (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Gene: atpA, MSMEG_4938, MSMEI_4811
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
Variant (production host): 4517
References: UniProt: A0R202, H+-transporting two-sector ATPase
#2: Protein ATP synthase subunit beta / / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 51670.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The N-terminus contains a hexaHis tag followed by a TEV site. Post-cleavage, GTATA would be the start of the mature protein.
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: atpD, MSMEG_4936, MSMEI_4809
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
Variant (production host): 4517
References: UniProt: A0R200, H+-transporting two-sector ATPase
#3: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 33439.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: atpG, MSMEG_4937, MSMEI_4810
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
Variant (production host): 4517 / References: UniProt: A0R201
#4: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 13277.741 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: atpC, MSMEG_4935, MSMEI_4808
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
Variant (production host): 4517 / References: UniProt: A0R1Z9

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Non-polymers , 4 types, 31 molecules

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


Mass: 427.201 Da / Num. of mol.: 5 / 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.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23% (w/v) polyethylene glycol (PEG) 4000, 300 mM magnesium formate and 100 mM Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→47 Å / Num. obs: 35040 / % possible obs: 99 % / Redundancy: 4.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.067 / Rrim(I) all: 0.142 / Net I/σ(I): 7 / Num. measured all: 149931 / Scaling rejects: 68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
4-4.240.5121857645900.7980.2850.5892.899
13.27-474.10.04411610150.9980.0230.04613.393.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0230refinement
MOSFLMdata reduction
Aimless0.5.28data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HKK

5hkk


Resolution: 4→45.59 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.841 / SU B: 103.841 / SU ML: 1.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3666 1666 4.8 %RANDOM
Rwork0.331 ---
obs0.3327 33246 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 287.97 Å2 / Biso mean: 161.472 Å2 / Biso min: 75.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.42 Å20 Å2
2--0.84 Å2-0 Å2
3----2.71 Å2
Refinement stepCycle: final / Resolution: 4→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23414 0 145 20 23579
Biso mean--146.82 137.62 -
Num. residues----3073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01423948
X-RAY DIFFRACTIONr_bond_other_d0.0010.01721920
X-RAY DIFFRACTIONr_angle_refined_deg0.7331.66332449
X-RAY DIFFRACTIONr_angle_other_deg0.6391.63551315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.50853048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.30521.9971252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99154071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.36715191
X-RAY DIFFRACTIONr_chiral_restr0.0270.23186
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0227077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024150
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A134130.09
12B134130.09
21A136290.08
22C136290.08
31B136060.08
32C136060.08
41D126540.1
42E126540.1
51D132660.08
52F132660.08
61E125510.11
62F125510.11
LS refinement shellResolution: 4→4.104 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 129 -
Rwork0.406 2388 -
all-2517 -
obs--98.05 %

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