[English] 日本語
Yorodumi
- PDB-3lmn: Oligomeric structure of the DUSP domain of human USP15 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lmn
TitleOligomeric structure of the DUSP domain of human USP15
ComponentsUbiquitin carboxyl-terminal hydrolase 15
KeywordsHYDROLASE / UCH / USP / DUB / DEUBIQUITYLATION / DEUBIQUITINATING ENZYME / UBIQUITIN / UBIQUITIN SPECIFIC PROTEASE / UBIQUITIN CARBOXYTERMINAL HYDROLASE / CLEAVAGE / USP15 / DUB15 / UBP15 / ENDOPEPTIDASE / THIOLESTERASE / DUSP / DOMAIN-SWAPPING / STRUCTURAL GENOMICS CONSORTIUM (SGC) / Acetylation / Alternative splicing / Phosphoprotein / Protease / Thiol protease / Ubl conjugation pathway
Function / homology
Function and homology information


regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / deubiquitinase activity / transforming growth factor beta receptor binding / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling ...regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / deubiquitinase activity / transforming growth factor beta receptor binding / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling / protein deubiquitination / SMAD binding / BMP signaling pathway / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal ...DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWalker, J.R. / Asinas, A. / Avvakumov, G.V. / Alenkin, D. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S.
CitationJournal: To be Published
Title: Crystal Structure of the Human Ubiquitin-Specific Protease 15 DUSP Domain
Authors: Walker, J.R. / Asinas, A. / Avvakumov, G.V. / Alenkin, D. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionJan 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1634
Polymers31,0572
Non-polymers1062
Water3,675204
1
A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,65316
Polymers124,2288
Non-polymers4248
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area25000 Å2
ΔGint-139 kcal/mol
Surface area49840 Å2
MethodPISA
2
A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3268
Polymers62,1144
Non-polymers2124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area10460 Å2
ΔGint-62 kcal/mol
Surface area26960 Å2
MethodPISA
3
A: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1634
Polymers31,0572
Non-polymers1062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area2950 Å2
ΔGint-21 kcal/mol
Surface area15760 Å2
MethodPISA
4
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1774
Polymers31,0572
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area3060 Å2
ΔGint-15 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.174, 138.174, 132.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 15 / Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 / Deubiquitinating enzyme 15 ...Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 / Deubiquitinating enzyme 15 / Unph-2 / Unph4


Mass: 15528.555 Da / Num. of mol.: 2 / Fragment: DUSP DOMAIN, RESIDUES 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0529, USP15 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R / References: UniProt: Q9Y4E8, EC: 3.1.2.15
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.75 Å3/Da / Density % sol: 73.88 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: Crystals of the dusp domain of usp15 were grown at 291.1 K using the sitting drop method by mixing equal volumes of protein solution (15 mg/ml) and crystallization buffer (2.0 M ammonium ...Details: Crystals of the dusp domain of usp15 were grown at 291.1 K using the sitting drop method by mixing equal volumes of protein solution (15 mg/ml) and crystallization buffer (2.0 M ammonium formate, 0.1 M sodium acetate, pH 3.8.) The crystals were cryoprotected by immersion in well solution supplemented with 20% (v/v) glycerol prior to dunking and storage in liquid nitrogen., VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 7, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 35029 / Num. obs: 35029 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Rsym value: 0.083 / Net I/σ(I): 35.89
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 3.62 / Num. unique all: 1727 / Rsym value: 0.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JYU

3jyu


Resolution: 2.15→19.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.484 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20401 1749 5 %RANDOM
Rwork0.18337 ---
obs0.18442 33132 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.241 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 7 204 2327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222222
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9533014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5185267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14824.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80515394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.241159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211699
X-RAY DIFFRACTIONr_mcbond_it0.5551.51321
X-RAY DIFFRACTIONr_mcangle_it1.0422121
X-RAY DIFFRACTIONr_scbond_it1.8773901
X-RAY DIFFRACTIONr_scangle_it2.8484.5893
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 130 -
Rwork0.211 2376 -
obs--100 %
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)
15.72182.249-2.72914.1915-0.52679.4919-0.0984-0.2162-0.5342-0.0479-0.1389-0.14860.79870.16930.23730.12070.02440.05510.08470.00360.112640.40224.356132.489
28.4054-0.7941-1.70983.1734-0.95196.4784-0.09520.304-0.2261-0.41910.0044-0.23260.43990.08550.09080.17670.01620.04740.1538-0.03140.09245.791210.744714.6568
32.8755-0.64070.45720.1466-0.22086.68290.00570.2111-0.0108-0.0109-0.04510.0145-0.0562-0.1370.03940.1688-0.01490.00780.1865-0.00630.17337.598916.071721.3187
46.9334-2.60832.0035.2419-5.62776.1579-0.1036-0.40730.45990.2129-0.0861-0.2097-0.21870.14040.18970.1263-0.01410.02050.204-0.05130.144137.28316.631835.6646
56.5817-2.78655.63412.9157-2.04195.2237-0.06910.01460.3329-0.0679-0.1023-0.3556-0.15430.26740.17130.1193-0.00920.06670.29180.00190.184544.22210.128441.1391
69.46193.69535.0451.60050.98898.8354-0.23140.04140.109-0.11750.09150.0230.0734-0.43950.140.12460.00980.04290.25910.02260.154940.181910.258546.5114
71.86380.6013-0.65693.9754-5.43278.6612-0.0707-0.02960.0690.3106-0.1248-0.0493-0.5555-0.3650.19550.13010.01940.03690.2438-0.0530.180630.601417.594535.371
818.60886.2831.369123.8769-0.09447.3956-0.42660.07881.8313-0.35030.12872.7571-1.1437-1.28220.29790.38030.1999-0.08810.53120.04130.782325.15129.522522.3557
920.13034.0141-0.360110.56120.32253.8097-0.38850.61060.9712-0.2076-0.19470.1228-0.8031-0.42740.58320.3170.0546-0.05970.2360.04520.250936.387130.890422.9978
1011.58433.36320.778916.30712.572113.1037-0.05720.310.0088-0.1543-0.1266-0.4264-0.11290.63180.18390.104-0.0063-0.00680.10870.01680.142243.083624.326427.383
113.5551.6214-0.51472.543-1.03755.6726-0.10750.1016-0.2845-0.1016-0.09060.0780.2802-0.23110.19810.0925-0.01840.01310.1176-0.0280.088133.281210.354926.7664
1214.8526-0.3168-8.59932.6281-2.148412.38530.09030.8695-0.0974-0.24-0.00050.4527-0.1109-1.2535-0.08980.08760.0049-0.05010.2515-0.01080.135929.014418.969821.1648
1318.35517.8599-2.25235.5294-1.65941.40780.21270.29790.9186-0.2801-0.16680.2389-0.1846-0.0007-0.04580.2440.03650.0320.21230.0590.179548.410821.094210.4596
145.1627-4.421-1.20793.78991.03260.28930.26460.19240.5923-0.1923-0.162-0.4874-0.0966-0.0235-0.10260.39890.03180.00050.27160.09610.399468.849621.13019.7098
1511.1614-3.14591.87133.8378-0.771112.9393-0.0697-0.28660.1390.17740.03190.1959-0.0877-0.03320.03780.21230.05560.06440.09530.0170.093353.21117.164420.0902
163.5732-4.04110.430810.49391.52371.674-0.0971-0.1874-0.30730.53830.17060.10660.00390.0036-0.07350.18680.01960.05950.09970.02990.108561.0855-3.097720.1128
175.3574-0.42421.177111.3322-4.15958.3384-0.02540.0444-0.81020.1603-0.04310.11510.1680.1110.06850.06560.02160.01840.0606-0.0930.293359.6627-13.525712.9612
183.1806-4.4524-0.807213.07927.53337.79890.11180.41270.3212-0.4950.038-0.3375-0.56910.3868-0.14980.2639-0.03720.01680.26670.00260.188560.64950.7895.9222
197.15693.52643.53433.54350.83013.7573-0.06820.4237-0.0084-0.0820.158-0.22470.09770.1281-0.08980.20740.02410.04440.13060.01420.107562.18446.484112.1197
2012.018-4.66764.17015.3983-2.27382.42870.05140.41950.1258-0.0141-0.0699-0.2868-0.00810.07320.01850.21420.02060.02990.10810.02610.050362.627813.317412.0162
212.0131-1.49211.02169.30051.68541.29720.14520.337-0.2085-0.72170.00870.0399-0.11480.1238-0.15390.33490.0073-0.00750.3693-0.02250.191155.21922.20843.6337
2225.83293.7143-10.4643.68255.382720.953-1.0513.2833-0.7476-0.49350.3460.39021.0535-1.3740.7051.31350.1179-0.43920.9916-0.39910.71453.9117-12.0055-6.5351
2317.83255.485.868615.52736.910918.13080.49461.2193-0.6511-0.6223-0.0501-0.45580.69120.8113-0.44450.30880.10940.05440.2591-0.1380.145466.5764-11.03290.2253
246.9345-1.609-1.61654.50130.21334.02370.09660.0457-0.61060.01850.06520.3210.02220.1444-0.16180.0909-0.02260.01110.04-0.0680.18858.5226-8.184711.8502
254.8146-1.29852.03679.97775.35199.08520.0160.3397-0.2616-0.4978-0.02460.6573-0.3199-0.4340.00860.1165-0.03120.00340.1593-0.02560.210449.6456-1.91338.7239
268.4684-8.59839.652512.3307-9.952411.04910.331-0.0961-0.5756-0.31390.19090.88220.413-0.1691-0.52190.2839-0.02870.01810.2357-0.14560.619356.7614-16.34517.8672
2758.9343-3.6007-24.71687.22441.523116.9875-0.30180.0709-0.85430.26830.05590.6838-0.2445-0.54070.24590.28920.0643-0.03950.1189-0.08680.201673.7382-23.85629.8537
287.6008-2.14984.06011.039-1.70262.88350.36690.5606-0.4667-0.2203-0.21470.06730.35110.3604-0.15220.2820.0339-0.02740.2028-0.06440.186792.8523-22.282413.3605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 20
2X-RAY DIFFRACTION2A21 - 26
3X-RAY DIFFRACTION3A27 - 35
4X-RAY DIFFRACTION4A36 - 41
5X-RAY DIFFRACTION5A42 - 51
6X-RAY DIFFRACTION6A52 - 57
7X-RAY DIFFRACTION7A58 - 71
8X-RAY DIFFRACTION8A72 - 78
9X-RAY DIFFRACTION9A79 - 83
10X-RAY DIFFRACTION10A84 - 89
11X-RAY DIFFRACTION11A90 - 107
12X-RAY DIFFRACTION12A108 - 116
13X-RAY DIFFRACTION13A117 - 122
14X-RAY DIFFRACTION14A123 - 133
15X-RAY DIFFRACTION15B5 - 10
16X-RAY DIFFRACTION16B11 - 24
17X-RAY DIFFRACTION17B25 - 34
18X-RAY DIFFRACTION18B35 - 38
19X-RAY DIFFRACTION19B39 - 49
20X-RAY DIFFRACTION20B50 - 58
21X-RAY DIFFRACTION21B59 - 70
22X-RAY DIFFRACTION22B71 - 78
23X-RAY DIFFRACTION23B79 - 87
24X-RAY DIFFRACTION24B88 - 98
25X-RAY DIFFRACTION25B99 - 110
26X-RAY DIFFRACTION26B111 - 118
27X-RAY DIFFRACTION27B119 - 123
28X-RAY DIFFRACTION28B124 - 133

+
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://pdbjlvh1.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