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- PDB-6ocd: Ricin A chain bound to VHH antibody V6D4 -

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Basic information

Entry
Database: PDB / ID: 6ocd
TitleRicin A chain bound to VHH antibody V6D4
Components
  • Ricin A chain
  • VHH antibody V6D4
KeywordsTOXIN
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.103 Å
AuthorsRudolph, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site.
Authors: Rudolph, M.J. / Czajka, T.F. / Davis, S.A. / Thi Nguyen, C.M. / Li, X.P. / Tumer, N.E. / Vance, D.J. / Mantis, N.J.
History
DepositionMar 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin A chain
B: VHH antibody V6D4
C: Ricin A chain
D: VHH antibody V6D4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,94413
Polymers84,3884
Non-polymers5569
Water5,423301
1
A: Ricin A chain
B: VHH antibody V6D4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4266
Polymers42,1942
Non-polymers2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ricin A chain
D: VHH antibody V6D4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5187
Polymers42,1942
Non-polymers3245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.937, 78.605, 103.890
Angle α, β, γ (deg.)90.000, 96.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Antibody , 2 types, 4 molecules ACBD

#1: Protein Ricin A chain


Mass: 28903.562 Da / Num. of mol.: 2 / Fragment: Toxin catalytic subunit, residues 40-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody VHH antibody V6D4


Mass: 13290.563 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 310 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6
Details: 100 mM MES (pH 6.0), 400 mM zinc acetate, and 11% PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 53563 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.076 / Rrim(I) all: 0.145 / Χ2: 0.967 / Net I/σ(I): 5.7 / Num. measured all: 193078
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.21.04926220.5180.6691.2480.65397.7
2.14-2.183.40.95826820.4950.6021.1350.67899.7
2.18-2.223.50.94126610.5420.5861.1110.66899.3
2.22-2.263.60.81726310.6630.5030.9620.701100
2.26-2.313.60.71327100.6810.4380.8390.69799.9
2.31-2.373.70.66226210.7520.4030.7760.739100
2.37-2.423.60.61926550.7440.3780.7270.70799.8
2.42-2.493.60.49927200.8250.3040.5850.725100
2.49-2.563.70.41626430.8660.2540.4880.74199.9
2.56-2.653.60.33326760.920.2030.3910.77599.9
2.65-2.743.60.27126850.9420.1660.3190.77799.8
2.74-2.853.70.21426500.9630.130.250.82999.9
2.85-2.983.70.16326880.9740.10.1920.85699.8
2.98-3.143.70.12726830.9830.0770.1490.92699.8
3.14-3.333.70.09626740.9890.0590.1131.07499.7
3.33-3.593.70.07726940.9910.0470.091.26699.8
3.59-3.953.70.06526650.9940.0390.0761.53599.8
3.95-4.523.70.05427080.9950.0330.0631.714100
4.52-5.73.60.04527330.9960.0280.0531.43100
5.7-503.60.04427620.9970.0270.0521.66299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å46.45 Å
Translation2.1 Å46.45 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.103→46.445 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.2
RfactorNum. reflection% reflection
Rfree0.2275 2606 4.87 %
Rwork0.1888 --
obs0.1907 53533 99.08 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 40.936 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 132.64 Å2 / Biso mean: 46.35 Å2 / Biso min: 14.56 Å2
Baniso -1Baniso -2Baniso -3
1-7.8677 Å2-0 Å2-8.2272 Å2
2---10.2445 Å20 Å2
3---2.3768 Å2
Refinement stepCycle: final / Resolution: 2.103→46.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5867 0 26 301 6194
Biso mean--49.73 44.42 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036070
X-RAY DIFFRACTIONf_angle_d0.6718240
X-RAY DIFFRACTIONf_chiral_restr0.049901
X-RAY DIFFRACTIONf_plane_restr0.0031087
X-RAY DIFFRACTIONf_dihedral_angle_d12.4862197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1027-2.1410.34561150.28222333244886
2.141-2.18210.33881290.26626712800100
2.1821-2.22670.31171390.25842703284299
2.2267-2.27510.30621500.242926262776100
2.2751-2.3280.27281430.229727292872100
2.328-2.38620.28211460.215626712817100
2.3862-2.45070.27561370.228626932830100
2.4507-2.52290.29581320.215626872819100
2.5229-2.60430.2691250.211326942819100
2.6043-2.69730.25081210.199127172838100
2.6973-2.80530.24561500.199526752825100
2.8053-2.9330.23061370.193326952832100
2.933-3.08760.23621260.194426942820100
3.0876-3.2810.26771270.17927282855100
3.281-3.53420.2171310.173127012832100
3.5342-3.88970.17651430.161627212864100
3.8897-4.45220.17161520.145127182870100
4.4522-5.60780.1831370.156927112848100
5.6078-46.45660.21121660.192827602926100
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)
10.66381.4184-1.10978.21410.38263.1836-0.32130.17240.7703-0.02620.1095-1.7336-0.29330.30430.16190.2444-0.0421-0.09150.22910.00510.42727.72228.8908-5.7289
28.83220.3238-3.03059.21112.43297.4663-0.10170.67960.3987-1.1023-0.00750.5229-0.19540.16050.15270.2373-0.0157-0.0370.25580.01960.165819.763327.2649-10.3043
33.68990.27141.71454.9460.78482.17630.08330.2198-0.3693-0.20790.1395-0.490.07930.1186-0.22670.20310.0220.01860.19960.01560.180422.845317.8002-4.746
44.8022-2.4142.34954.39261.90747.77360.0066-0.12280.03820.69950.0513-0.20220.3193-0.1392-0.04150.24410.0123-0.04720.14120.01150.254926.122718.26087.2788
53.9503-3.46-0.30693.9041.45095.5375-0.0021-0.1662-0.44250.73670.188-0.30380.39780.2881-0.20040.35940.0464-0.12210.21360.01630.438530.69515.35349.389
68.40.3349-1.63592.4597-1.67697.12310.0293-0.90490.15590.79990.09070.721-0.0225-0.5923-0.03220.36280.0140.0130.383-0.09040.230412.092228.094412.7221
78.50811.73475.28314.3894-1.52447.919-0.2585-0.34940.40090.8174-0.139-0.7359-0.85540.06530.41220.4335-0.004-0.13750.2207-0.08820.438126.937934.4199.8414
82.9421.53282.64444.03232.5967.96050.0114-0.16810.16380.50090.0147-0.02840.03140.13930.01720.29050.0526-0.02070.2323-0.04130.269917.963527.90036.6667
93.50882.0604-0.07967.89190.38074.6474-0.1523-0.15830.7974-0.17570.15810.7158-0.5106-0.3267-0.01040.27270.091-0.0770.2962-0.03980.41039.984434.6516-3.3384
103.1004-2.2742-0.26836.62336.27989.36240.1362-0.3189-0.02220.3771-0.08210.35160.4948-0.34090.00590.1672-0.06590.03110.26890.01980.25245.025516.83950.015
116.5134-1.448-0.64976.6713.72799.1776-0.1787-0.12110.56420.61660.10140.89260.8225-0.86650.03490.2744-0.05330.01880.5748-0.07770.5328-3.727218.5524-2.8
127.1725-0.68471.50425.3216-2.93595.73060.46-0.1427-0.35890.1262-0.36790.8060.3402-0.602-0.03760.2385-0.084-0.02390.2844-0.07580.33243.205415.0715-6.6168
132.2974-1.62012.49923.9189-1.67086.74080.229-1.1959-0.83780.7026-0.02170.51970.8048-0.8089-0.19390.7476-0.16440.04360.77970.20070.53679.77282.393618.0578
142.6185-3.44710.01394.64550.01220.0094-0.6034-0.3336-1.04280.93880.09310.95380.8493-0.57990.40870.9507-0.37050.14271.30330.20660.62271.3793-0.391619.5548
153.8739-0.82182.17275.9715-2.51839.3190.0245-0.8373-0.06860.9383-0.274-0.47930.1412-0.48820.19820.4518-0.1512-0.01050.57290.0780.388811.32597.919616.9084
165.0957-0.23291.26035.4768-1.50732.37070.1822-0.0482-0.3318-0.2990.04320.84570.511-0.2804-0.15490.2648-0.0705-0.03080.20830.03970.255-10.450137.975242.5168
170.6249-1.11110.35524.6654-3.24594.8029-0.0084-0.0115-0.03580.26920.22990.3308-0.2283-0.3273-0.26880.1125-0.01150.0050.2095-0.01350.2365-7.587848.140844.0172
185.1162-2.67113.10966.33680.91125.3233-0.2451-0.14330.42870.75980.2783-0.5504-0.38950.0683-0.05190.2706-0.00120.03170.1826-0.02030.24981.253449.243855.0593
192.4449-1.03711.76373.4119-0.62455.64330.24390.1661-0.2409-0.3806-0.1712-0.28020.74090.4157-0.1030.29050.07160.03330.21360.02360.2795.335235.174542.6815
206.7495-2.83021.19493.6482-1.86924.2035-0.09660.59460.1459-0.3196-0.2779-0.15330.31050.55890.40220.2523-0.01650.01060.27710.02450.2145.175749.751825.7867
213.00171.7012-1.70235.19782.67714.6469-0.11550.33120.0329-0.0965-0.16260.1009-0.20910.09520.25840.3220.0266-0.06940.29150.0640.2054-1.010852.118725.7103
229.48762.11133.42364.4232.99277.23230.07470.7896-0.1898-0.22410.2802-0.6476-0.03190.8441-0.34760.3873-0.1388-0.08660.43140.06180.530121.732761.867939.2554
237.72083.4121-4.88151.9993-6.57785.3540.2401-1.0135-0.17010.9384-0.5337-0.2532-1.2030.92570.20750.5906-0.1984-0.10980.6153-0.02280.500513.7858.211253.6023
244.10451.4756-1.69452.04882.56198.02010.1584-0.00530.3774-0.29710.01110.9641-0.7706-0.6118-0.08610.5994-0.1436-0.14520.40790.04130.649713.234269.871244.6756
258.60010.6247-1.66138.44343.52966.7493-0.01990.98440.441-0.1970.2675-0.5896-1.03880.3803-0.24750.4115-0.1786-0.03990.49360.10780.49322.098368.655939.8962
267.36513.2136.53084.24963.26847.51990.11740.12620.09010.5359-0.1861-0.3603-0.22430.33250.04970.3317-0.1445-0.0860.3860.08140.4615.523859.321443.0411
278.81447.22796.67415.91625.47595.04490.98910.4803-1.3211.4541-0.3287-0.56080.79560.8793-0.89260.683-0.0355-0.35230.68450.08010.864430.553457.417853.2781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:17)A5 - 17
2X-RAY DIFFRACTION2chain 'A' and (resseq 18:32)A18 - 32
3X-RAY DIFFRACTION3chain 'A' and (resseq 33:75)A33 - 75
4X-RAY DIFFRACTION4chain 'A' and (resseq 76:97)A76 - 97
5X-RAY DIFFRACTION5chain 'A' and (resseq 98:122)A98 - 122
6X-RAY DIFFRACTION6chain 'A' and (resseq 123:140)A123 - 140
7X-RAY DIFFRACTION7chain 'A' and (resseq 141:160)A141 - 160
8X-RAY DIFFRACTION8chain 'A' and (resseq 161:180)A161 - 180
9X-RAY DIFFRACTION9chain 'A' and (resseq 181:201)A181 - 201
10X-RAY DIFFRACTION10chain 'A' and (resseq 202:220)A202 - 220
11X-RAY DIFFRACTION11chain 'A' and (resseq 221:238)A221 - 238
12X-RAY DIFFRACTION12chain 'A' and (resseq 239:261)A239 - 261
13X-RAY DIFFRACTION13chain 'B' and (resseq 3:73)B3 - 73
14X-RAY DIFFRACTION14chain 'B' and (resseq 74:83)B74 - 83
15X-RAY DIFFRACTION15chain 'B' and (resseq 84:120)B84 - 120
16X-RAY DIFFRACTION16chain 'C' and (resseq 5:32)C5 - 32
17X-RAY DIFFRACTION17chain 'C' and (resseq 33:75)C33 - 75
18X-RAY DIFFRACTION18chain 'C' and (resseq 76:122)C76 - 122
19X-RAY DIFFRACTION19chain 'C' and (resseq 123:201)C123 - 201
20X-RAY DIFFRACTION20chain 'C' and (resseq 202:238)C202 - 238
21X-RAY DIFFRACTION21chain 'C' and (resseq 239:262)C239 - 262
22X-RAY DIFFRACTION22chain 'D' and (resseq 4:38)D4 - 38
23X-RAY DIFFRACTION23chain 'D' and (resseq 39:48)D39 - 48
24X-RAY DIFFRACTION24chain 'D' and (resseq 49:64)D49 - 64
25X-RAY DIFFRACTION25chain 'D' and (resseq 65:83)D65 - 83
26X-RAY DIFFRACTION26chain 'D' and (resseq 84:116)D84 - 116
27X-RAY DIFFRACTION27chain 'D' and (resseq 117:125)D117 - 125

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