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- PDB-6qss: Crystal Structure of Ignicoccus islandicus malate dehydrogenase c... -

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Basic information

Entry
Database: PDB / ID: 6qss
TitleCrystal Structure of Ignicoccus islandicus malate dehydrogenase co-crystallized with 10 mM Tb-Xo4
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Ignicoccus islandicus / malate dehydrogenase / Tb-Xo4
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / carboxylic acid metabolic process
Similarity search - Function
L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tb-Xo4 / TERBIUM(III) ION / Malate dehydrogenase
Similarity search - Component
Biological speciesIgnicoccus islandicus DSM 13165 (archaea)
MethodX-RAY DIFFRACTION / SOLUTION SCATTERING / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsRoche, J. / Girard, E. / Madern, D.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE11-0011 France
CitationJournal: J.Struct.Biol. / Year: 2019
Title: The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization.
Authors: Roche, J. / Girard, E. / Mas, C. / Madern, D.
History
DepositionFeb 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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
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_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,45127
Polymers134,3714
Non-polymers4,08023
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17850 Å2
ΔGint-172 kcal/mol
Surface area44990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.486, 109.017, 151.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Malate dehydrogenase /


Mass: 33592.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ignicoccus islandicus DSM 13165 (archaea)
Gene: EYM_03995 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U3FQH7
#2: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#3: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Tb
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
SOLUTION SCATTERING

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes pH 7, 10% w/v PEG 6000. Tb-Xo4 was directly mixed with the protein solution at a final concentration of 10 mM prior to crystallization.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.892→45.92 Å / Num. obs: 103746 / % possible obs: 99.17 % / Redundancy: 7.4 % / Biso Wilson estimate: 30.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1146 / Rpim(I) all: 0.04477 / Net I/σ(I): 12.92
Reflection shellResolution: 1.892→1.96 Å / Redundancy: 7.1 % / Num. unique obs: 9531 / CC1/2: 0.637 / Rpim(I) all: 0.4782 / % possible all: 92.41

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BGU
Resolution: 1.892→45.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.147 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.233 5161 4.98 %RANDOM
Rwork0.205 ---
obs0.206 103697 99.2 %-
Displacement parametersBiso mean: 38.53 Å2
Baniso -1Baniso -2Baniso -3
1--12.7375 Å20 Å20 Å2
2--6.5967 Å20 Å2
3---6.1408 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.892→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9236 0 81 308 9625
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0512882HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3339SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1609HARMONIC5
X-RAY DIFFRACTIONt_it9481HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion16.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1330SEMIHARMONIC5
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_contact11504SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.91 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3579 -4.1 %
Rwork0.2771 1989 -
all0.2803 2074 -
obs--73.65 %
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)
11.4247-0.073-0.44851.7471-0.89161.9586-0.04160.0819-0.029-0.096-0.0346-0.13110.23650.15670.0762-0.07310.0101-0.02-0.10080.0022-0.07826.520718.90937.5393
21.69460.0888-0.58760-0.97621.91960.03020.1319-0.0464-0.20510.0187-0.06410.14750.248-0.04890.14880.09050.1824-0.1571-0.0342-0.180434.645622.604117.1806
31.1524-0.1283-0.73871.09030.29560.0572-0.04080.1508-0.0378-0.27070.085-0.02810.18480.1171-0.04420.0496-0.0110.009-0.01960.0078-0.101125.117125.122619.9431
40.80650.03670.1453.43120.75273.1528-0.04510.0630.14330.1066-0.0057-0.29310.09010.22980.0508-0.1468-0.0330.0018-0.04570.0135-0.024329.400846.907331.6556
50.40571.93871.662600.76571.2480.0175-0.00470.0999-0.03940.03860.0168-0.25960.1724-0.0560.0277-0.04510.0431-0.1132-0.02350.011326.805661.560236.4945
62.48982.10530.42731.8860.75031.34570.05670.0291-0.02680.00750.0676-0.114-0.02380.1743-0.1243-0.1438-0.06450.02-0.02330.0333-0.017340.536746.995233.4237
70.88620.09691.74722.1579-0.51021.7944-0.0132-0.043900.05490.05510.0518-0.09070.0273-0.0419-0.03030.00940.02710.00620.0242-0.054524.100731.943634.5446
80.53690.35610.03832.43280.91261.7616-0.01560.27350.1756-0.57620.03470.1886-0.16130.0314-0.0191-0.03030.02870.0204-0.03980.0416-0.130620.95537.659219.0911
92.57870.07662.46111.68362.6422.25880.01670.1293-0.0605-0.1492-0.0165-0.005-0.1028-0.0537-0.0002-0.0121-0.0069-0.0171-0.0193-0.0048-0.012918.878146.003619.7487
100.0375-2.7204-2.13570.00113.28222.5505-0.04010.18190.0268-0.1398-0.0278-0.0243-0.02180.05390.06790.01410.00010.0896-0.0340.0174-0.105231.021740.947211.9838
110.15580.4379-0.74860-2.72114.11610.03130.04070.09850.2993-0.1434-0.204-0.21760.0630.1122-0.0164-0.0706-0.0447-0.0951-0.0814-0.098533.33634.05352.1906
120.2087-2.12210.3952.2365-2.89762.97040.09060.01760.04540.5454-0.2397-0.0917-0.51380.35750.1491-0.0244-0.1002-0.0337-0.1264-0.0128-0.142337.366338.665345.7289
130.0216-0.64172.22220-1.30882.20770.0313-0.0788-0.01440.2308-0.063-0.0461-0.23540.07570.03170.1902-0.1898-0.0942-0.0745-0.0554-0.102740.743842.180552.3145
143.1183-2.2670.94520.8462-3.41311.94020.0270.00860.16530.0155-0.1937-0.1933-0.12550.58160.16670.0501-0.2258-0.1704-0.1020.0714-0.253249.405627.271361.2483
150.43450.57280.03511.3662-0.26262.0823-0.0182-0.0337-0.15740.2851-0.0576-0.2029-0.27380.37830.0758-0.0699-0.0614-0.0679-0.0990.0059-0.138633.844818.201162.4133
160.8241.91762.08660.0308-0.55871.5228-0.0112-0.0675-0.16190.06620.08070.04820.02320.0263-0.0695-0.0955-0.07630.0698-0.1153-0.03430.165915.50121.59459.1876
171.8963-1.1208-1.75011.9602-0.25843.7777-0.01650.0199-0.10190.0003-0.0767-0.05230.22480.0980.0932-0.1280.0429-0.0315-0.0941-0.07470.01333.86695.951551.3485
180.45220.2379-2.50380-0.45461.69250.01150.1330.09970.2883-0.1057-0.0936-0.24540.15160.09430.0421-0.0578-0.0626-0.0498-0.0061-0.124130.846727.30556.5328
193.0752-0.06771.15991.61130.27463.22270.0609-0.12090.04590.4896-0.074-0.1032-0.34640.16120.01310.0974-0.0972-0.0612-0.12830.0139-0.189531.970822.071671.7272
202.10210.53631.09442.0845-1.5350.0854-0.0257-0.043-0.07720.3052-0.0172-0.0162-0.02170.2230.04290.0453-0.0544-0.1121-0.042-0.0083-0.170739.40211.696673.6923
210-0.73440.69311.5771-1.05921.36430.03940.03190.01930.06840.07740.19740.108-0.2108-0.1168-0.0593-0.04850.0106-0.088-0.0116-0.0849-0.123326.315650.1904
221.4974-0.123-2.03710.5542-0.79221.83680.0415-0.04-0.03260.08640.13330.25150.0161-0.2071-0.1749-0.0008-0.05430.0708-0.1096-0.0062-0.1003-7.34322.975967.7843
232.16871.88521.00790.0527-0.50341.7815-0.052-0.1221-0.00750.01270.1950.13210.276-0.297-0.1430.062-0.02690.0443-0.1370.071-0.1576-2.847416.224568.4281
241.45630.6753-0.04392.4574-1.09262.0084-0.0985-0.26720.33620.38960.04440.2481-0.3519-0.22720.05410.12020.0322-0.0006-0.1833-0.0695-0.180513.626836.822573.8963
250.89082.0969-0.58992.0246-0.84751.9216-0.0053-0.11670.06460.1488-0.0429-0.0422-0.09680.0770.04810.2719-0.104-0.1153-0.1706-0.0963-0.107726.1245.166377.8283
261.6341-1.22740.77033.1493-0.6651.46550.0525-0.04310.1930.41260.07370.157-0.2118-0.1731-0.12620.18660.10220.058-0.1637-0.1013-0.19796.21645.206775.1469
273.4542-1.14610.39461.5798-0.76180.55730.00520.0099-0.01750.15460.04690.0658-0.1647-0.0256-0.05210.024-0.00530.0208-0.11240.0002-0.13039.27627.937761.9693
283.30721.4389-1.64470.1020.04881.55310.0005-0.27220.01680.1882-0.0319-0.0116-0.02260.10390.03140.1170.03030.0158-0.094-0.0111-0.165610.345218.928376.213
290.00020.7885-0.639401.855400.0191-0.2375-0.1060.1971-0.0918-0.0532-0.05210.06020.07270.2718-0.0259-0.0089-0.1236-0.053-0.336915.678225.247883.9364
3000.7231-0.15530.5709-1.97551.91330.0087-0.0435-0.0750.04460.01710.0551-0.0551-0.0136-0.02580.15890.06150.10090.0096-0.0906-0.2238-2.789519.696184.6329
310.19080.22080.51211.8414-1.91183.2560.0033-0.0480.06080.3184-0.05860.0218-0.27140.04270.0552-0.03920.00390.0062-0.1431-0.0764-0.0887.731448.120855.2563
322.8272-1.46431.62881.8384-2.48872.782-0.0116-0.03110.16010.21930.2956-0.0179-0.4295-0.2772-0.2840.0210.16160.0394-0.0951-0.015-0.1115-7.244260.763541.9997
330.0122-0.78670.39771.7832-1.16143.5634-0.0561-0.01020.0430.23910.00260.1399-0.5084-0.06520.0536-0.00530.0266-0.0281-0.1135-0.0285-0.04882.603858.319939.5001
341.79621.57370.28542.08720.23632.34170.0043-0.1328-0.09450.1538-0.03580.12710.1448-0.14330.0315-0.0812-0.0104-0.0132-0.01650.0223-0.0447-1.269333.6634.2816
351.3018-0.77740.15781.74650.7721.49570.0183-0.03580.0137-0.08560.01160.10720.0582-0.2045-0.03-0.0895-0.0051-0.0185-0.07970.0116-0.0340.557133.51126.7904
361.0142-0.60350.73980.6232.38992.4697-0.0277-0.0361-0.0077-0.2015-0.0430.03490.3008-0.16770.0708-0.0401-0.04190.0227-0.04310.13180.0092-5.908523.983823.8738
371.34890.8510.132.017-0.37712.0148-0.0137-0.12290.11530.1660.07570.3103-0.0723-0.3482-0.0619-0.07380.0280.0209-0.06850.0011-0.03180.407239.491742.0328
380.5247-0.13631.54791.5529-0.40990.6976-0.06150.1062-0.0282-0.08520.01140.0515-0.2530.07510.0502-0.04730.01220.0057-0.02120.0181-0.0455.213151.441228.4217
392.88441.6250.56034.41650.58550.09050.00210.18710.1356-0.33210.033-0.102-0.09420.1327-0.0351-0.01880.04590.0242-0.03830.0411-0.09672.395144.806719.5308
402.6591-0.71791.44711.4801-0.2410.9653-0.05960.03360.2096-0.13670.04260.00960.0537-0.2440.017-0.07620.031-0.058-0.04810.04940.038-7.750557.334226.1073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - 85 }
2X-RAY DIFFRACTION2{ A|90 - 112 }
3X-RAY DIFFRACTION3{ A|113 - 145 }
4X-RAY DIFFRACTION4{ A|146 - 191 }
5X-RAY DIFFRACTION5{ A|192 - 207 }
6X-RAY DIFFRACTION6{ A|208 - 227 }
7X-RAY DIFFRACTION7{ A|228 - 251 }
8X-RAY DIFFRACTION8{ A|252 - 278 }
9X-RAY DIFFRACTION9{ A|279 - 289 }
10X-RAY DIFFRACTION10{ A|290 - 308 }
11X-RAY DIFFRACTION11{ B|3 - 29 }
12X-RAY DIFFRACTION12{ B|30 - 58 }
13X-RAY DIFFRACTION13{ B|59 - 72 }
14X-RAY DIFFRACTION14{ B|73 - 113 }
15X-RAY DIFFRACTION15{ B|114 - 190 }
16X-RAY DIFFRACTION16{ B|191 - 206 }
17X-RAY DIFFRACTION17{ B|207 - 229 }
18X-RAY DIFFRACTION18{ B|230 - 248 }
19X-RAY DIFFRACTION19{ B|249 - 282 }
20X-RAY DIFFRACTION20{ B|283 - 309 }
21X-RAY DIFFRACTION21{ C|2 - 69 }
22X-RAY DIFFRACTION22{ C|70 - 99 }
23X-RAY DIFFRACTION23{ C|100 - 145 }
24X-RAY DIFFRACTION24{ C|146 - 190 }
25X-RAY DIFFRACTION25{ C|191 - 207 }
26X-RAY DIFFRACTION26{ C|208 - 227 }
27X-RAY DIFFRACTION27{ C|228 - 253 }
28X-RAY DIFFRACTION28{ C|254 - 279 }
29X-RAY DIFFRACTION29{ C|280 - 297 }
30X-RAY DIFFRACTION30{ C|298 - 309 }
31X-RAY DIFFRACTION31{ D|3 - 81 }
32X-RAY DIFFRACTION32{ D|90 - 112 }
33X-RAY DIFFRACTION33{ D|113 - 144 }
34X-RAY DIFFRACTION34{ D|145 - 164 }
35X-RAY DIFFRACTION35{ D|165 - 199 }
36X-RAY DIFFRACTION36{ D|200 - 214 }
37X-RAY DIFFRACTION37{ D|215 - 251 }
38X-RAY DIFFRACTION38{ D|252 - 279 }
39X-RAY DIFFRACTION39{ D|280 - 293 }
40X-RAY DIFFRACTION40{ D|294 - 309 }

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