[English] 日本語
Yorodumi
- PDB-5odc: Heterodisulfide reductase / [NiFe]-hydrogenase complex from Metha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5odc
TitleHeterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus at 2.3 A resolution
Components
  • (Heterodisulfide reductase, subunit ...) x 3
  • (Methyl-viologen reducing hydrogenase subunit ...) x 3
KeywordsOXIDOREDUCTASE / Heterodisulfide reductase / [NiFe]-hydrogenase / FeS cluster / ferredoxin / CCG motif / methanogenesis / flavoprotein / flavin-based electron bifurcation / [2Fe-2S] cluster / macromolecular complex / anaerobic / thioredoxin / metabolism
Function / homology
Function and homology information


dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / hydrogenase (acceptor) / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding ...dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / hydrogenase (acceptor) / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
4Fe-4S dicluster domain / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / : / Methyl-viologen-reducing hydrogenase, delta subunit ...4Fe-4S dicluster domain / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / : / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / 4Fe-4S dicluster domain / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / FAD-dependent oxidoreductase 2, FAD binding domain / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Alpha-helical ferredoxin / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / FAD binding domain / Pyridine nucleotide-disulphide oxidoreductase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Heterodisulfide reductase, subunit C / Methyl-viologen reducing hydrogenase subunit D / Methyl-viologen reducing hydrogenase subunit G ...Non-cubane [4Fe-4S]-cluster / ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Heterodisulfide reductase, subunit C / Methyl-viologen reducing hydrogenase subunit D / Methyl-viologen reducing hydrogenase subunit G / Methyl-viologen reducing hydrogenase subunit A / Heterodisulfide reductase, subunit B / CoB--CoM heterodisulfide reductase iron-sulfur subunit A
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWagner, T. / Koch, J. / Ermler, U. / Shima, S.
CitationJournal: Science / Year: 2017
Title: Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
Authors: Wagner, T. / Koch, J. / Ermler, U. / Shima, S.
History
DepositionJul 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heterodisulfide reductase, subunit A
B: Heterodisulfide reductase, subunit B
C: Heterodisulfide reductase, subunit C
D: Methyl-viologen reducing hydrogenase subunit D
E: Methyl-viologen reducing hydrogenase subunit G
F: Methyl-viologen reducing hydrogenase subunit A
G: Heterodisulfide reductase, subunit A
H: Heterodisulfide reductase, subunit B
I: Heterodisulfide reductase, subunit C
J: Methyl-viologen reducing hydrogenase subunit D
K: Methyl-viologen reducing hydrogenase subunit G
L: Methyl-viologen reducing hydrogenase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,76372
Polymers451,69812
Non-polymers14,06560
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79310 Å2
ΔGint-905 kcal/mol
Surface area124180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)378.047, 98.446, 137.884
Angle α, β, γ (deg.)90.00, 110.70, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Heterodisulfide reductase, subunit ... , 3 types, 6 molecules AGBHCI

#1: Protein Heterodisulfide reductase, subunit A


Mass: 71591.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GB ref WP_018154264.1
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TCB9*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#2: Protein Heterodisulfide reductase, subunit B


Mass: 32075.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GB ref WP_018154154.1, This subunit contains two pentacoordinated non cubane [4Fe-4S] cluster
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TCB4*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#3: Protein Heterodisulfide reductase, subunit C


Mass: 20483.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GB ref WP_018154153.1, The C-terminus is too flexible to be modeled in the electron density
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TC97*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase

-
Methyl-viologen reducing hydrogenase subunit ... , 3 types, 6 molecules DJEKFL

#4: Protein Methyl-viologen reducing hydrogenase subunit D


Mass: 16057.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GB ref WP_018154260.1
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TC98*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#5: Protein Methyl-viologen reducing hydrogenase subunit G


Mass: 32511.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GB ref WP_018154261.1
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TC99*PLUS, hydrogenase (acceptor)
#6: Protein Methyl-viologen reducing hydrogenase subunit A


Mass: 53129.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GB ref WP_018154262.1, The C-terminus has been post-translationally cleaved
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TCA6*PLUS, hydrogenase (acceptor)

-
Non-polymers , 13 types, 892 molecules

#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#11: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Fe4S4
#12: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#13: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Fe4S4
#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#15: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#16: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#17: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#18: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3HFeN2NiO
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 % / Description: Black thick plate square shape.
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution. The best-diffracting crystals were obtained using the sitting drop method in a crystallization ...Details: Crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution. The best-diffracting crystals were obtained using the sitting drop method in a crystallization plate (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular Dimensions, Suffolk, UK); the crystallization reservoir contained 100 mM Tris/HCl, pH 8.5, 30% (w/v) polyethylene glycol 4000, and 200 mM Na acetate trihydrate. Crystallization drop contained 1 ul HdrABC-MvhAGD at 25 mg/ml premixed with 2 mM FAD and 1 ul of precipitant. The crystals appear after 1-2 weeks and are cryoprotected in the crystallization solution supplemented with 30% glycerol.
PH range: 8-8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.733 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.733 Å / Relative weight: 1
ReflectionResolution: 2.3→49.22 Å / Num. obs: 204479 / % possible obs: 97.4 % / Redundancy: 8.5 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.053 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 25173 / CC1/2: 0.5 / Rpim(I) all: 0.282 / % possible all: 83

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→49.22 Å / Cor.coef. Fo:Fc: 0.9452 / Cor.coef. Fo:Fc free: 0.9336 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.256 / SU Rfree Blow DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 10353 5.06 %RANDOM
Rwork0.1778 ---
obs0.1789 204471 97.28 %-
Displacement parametersBiso mean: 49.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.6268 Å20 Å20.5811 Å2
2--1.8038 Å20 Å2
3----4.4305 Å2
Refine analyzeLuzzati coordinate error obs: 0.296 Å
Refinement stepCycle: 1 / Resolution: 2.3→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61847 0 1504 832 64183
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00563156HARMONIC5
X-RAY DIFFRACTIONt_angle_deg1114761HARMONIC5
X-RAY DIFFRACTIONt_dihedral_angle_d14270SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes819HARMONIC2
X-RAY DIFFRACTIONt_gen_planes9008HARMONIC20
X-RAY DIFFRACTIONt_it63156HARMONIC20
X-RAY DIFFRACTIONt_nbd31SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.79
X-RAY DIFFRACTIONt_other_torsion14.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4127SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact70649SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2708 578 4.91 %
Rwork0.2487 11192 -
all0.2498 11770 -
obs--97.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.50230.1359-0.12880.0755-0.03410.0483-0.0206-0.0272-0.15130.02330.0386-0.0423-0.0241-0.0008-0.018-0.11460.03030.0071-0.1088-0.00710.2362120.681673.117927.5581
20.92360.3029-0.07241.59390.26290.00170.00580.040.02910.04380.0075-0.0147-0.0750.085-0.0133-0.0306-0.03630.0435-0.14650.0270.1175161.0633121.5161.8766
30.91040.2703-0.17980.8357-0.39320.21020.00340.05330.0028-0.0434-0.00810.0075-0.02770.02110.0047-0.054-0.06380.0647-0.0248-0.02630.0755154.6765106.821-9.9618
41.80670.2295-0.03360.895-0.12430.0116-0.00920.06320.03640.01140.02830.0067-0.0118-0.013-0.0191-0.0780.00330.0253-0.00170.02010.081193.573783.330232.5709
51.14190.1253-0.37460.00290.00620.3468-0.0121-0.00420.00360.06760.0328-0.0270.0234-0.0301-0.0208-0.06480.03240.0243-0.01570.04680.050469.974773.086651.0503
60.79830.154-0.14630.426-0.13410.176-0.02260.0878-0.06260.0320.09850.07840.0932-0.2075-0.0759-0.1363-0.0270.02890.08030.11260.062745.495267.059151.0458
70.338-0.184-0.07570-0.00290.125-0.0082-0.1140.027-0.0180.0424-0.0254-0.04490.0341-0.0341-0.13680.0104-0.0121-0.0852-0.03150.2461145.472985.048432.5376
81.85010.29810.896101.11530.413-0.0222-0.0292-0.0305-0.09010.01220.01170.0654-0.1230.0099-0.0727-0.0635-0.03370.09690.0119-0.026897.18585.227-15.4215
91.2984-0.23310.09920.2244-0.0779-0.11050.00450.0235-0.0048-0.02420.0059-0.0341-0.0196-0.0672-0.0105-0.04630.1056-0.00660.03420.05530.0353104.2105101.765-6.843
100.973-0.20310.24430.5081-0.3870.0926-0.02360.0280.0433-0.02340.01150.0237-0.00560.02940.0121-0.1571-0.0093-0.0014-0.0290.02380.1897171.888678.898220.6573
111.8805-0.10740.39890.0017-0.0960.033-0.05540.00970.04390.0197-0.03290.02760.03940.04030.0882-0.17530.0027-0.0177-0.05710.09230.1469198.656768.146133.0624
121.1509-0.1130.09230.4790.16870.3277-0.06550.02690.14090.0432-0.0142-0.0409-0.04240.20810.0796-0.2578-0.0608-0.05380.07090.13740.1307223.538671.846834.3337
130.2569-0.1768-0.1340.1189-0.0713-0.03990.00060.00330.0108-0.00280.00320.0033-0.00540.0063-0.00380.01110.00390.003-0.00650.00860.0115132.744781.08827.0564
140.7406-0.0550.04250.153-0.0024-0.00430.0111-0.0659-0.0287-0.0116-0.0118-0.0720.01130.04620.0007-0.1090.03820.0262-0.0566-0.03110.0731133.22778.081231.3789
152.2271-0.1224-0.54130.4553-0.46680.7489-0.0039-0.0294-0.00450.0231-0.00120.0060.0077-0.00310.00510.0133-0.0027-0.00590.00790.00640.0069139.765483.457326.4581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }
13X-RAY DIFFRACTION13{ P|* }
14X-RAY DIFFRACTION14{ W|* }
15X-RAY DIFFRACTION15{ Z|* }

+
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