[English] 日本語
Yorodumi
- PDB-8r21: Alpha-1-antitrypsin (Ile340Trp) in the native conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r21
TitleAlpha-1-antitrypsin (Ile340Trp) in the native conformation
ComponentsAlpha-1-antitrypsin
KeywordsPROTEIN BINDING / Antitrypsin / protease inhibitor / serpin / mutant / deficiency / small molecule
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation ...Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / : / protease binding / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsAldobiyan, I. / Lee, H.J. / Lomas, D.A. / Irving, J.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V034243/1 United Kingdom
Other governmentNIHR investigator award to DAL
Other privateAlpha-1 Foundation to JAI 1036784
CitationJournal: To be published
Title: Structural determinants of instability in alpha-1-antitrypsin
Authors: Aldobiyan, I. / Lee, H.J. / Irving, J.A. / Lomas, D.A.
History
DepositionNov 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-1-antitrypsin
B: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)91,3702
Polymers91,3702
Non-polymers00
Water18010
1
A: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,6851
Polymers45,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,6851
Polymers45,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.450, 113.450, 136.743
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 24 through 25 and (name N...
d_2ens_1(chain "B" and (resid 24 through 25 or resid 28...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNLYSLYSAA24 - 2534 - 35
d_12PROPROPROPROAA2838
d_13LEULEUPHEPHEAA30 - 3540 - 45
d_14LEULEUTYRTYRAA37 - 3847 - 48
d_15ALAALAALAALAAA4252
d_16ILEILEPROPROAA50 - 5460 - 64
d_17ILEILEALAALAAA57 - 6267 - 72
d_18LEULEUTHRTHRAA64 - 6874 - 78
d_19ALAALAALAALAAA7080
d_110THRTHRASPASPAA72 - 7482 - 84
d_111ILEILEGLYGLYAA76 - 7986 - 89
d_112GLUGLUGLUGLUAA8696
d_113ALAALAGLNGLNAA90 - 91100 - 101
d_114HISHISGLNGLNAA93 - 97103 - 107
d_115LEULEULEULEUAA100110
d_116THRTHRTHRTHRAA114124
d_117GLYGLYGLYGLYAA117127
d_118PHEPHESERSERAA119 - 121129 - 131
d_119LEULEULEULEUAA124134
d_120LYSLYSLEULEUAA129 - 131139 - 141
d_121TYRTYRTYRTYRAA138148
d_122ALAALAALAALAAA142152
d_123THRTHRVALVALAA144 - 145154 - 155
d_124PHEPHEPHEPHEAA147157
d_125ILEILEILEILEAA157167
d_126VALVALVALVALAA161171
d_127GLYGLYGLYGLYAA164174
d_128GLNGLNILEILEAA166 - 169176 - 179
d_129ARGARGTHRTHRAA178 - 180188 - 190
d_130PHEPHEALAALAAA182 - 183192 - 193
d_131VALVALPHEPHEAA185 - 190195 - 200
d_132LYSLYSGLUGLUAA193 - 195203 - 205
d_133PROPROPROPROAA197207
d_134THRTHRTHRTHRAA203213
d_135GLUGLUHISHISAA206 - 209216 - 219
d_136THRTHRTHRTHRAA214224
d_137VALVALMETMETAA216 - 221226 - 231
d_138GLYGLYMETMETAA225 - 226235 - 236
d_139ASNASNASNASNAA228238
d_140SERSERSERSERAA236 - 237246 - 247
d_141VALVALVALVALAA239249
d_142LEULEULEULEUAA241251
d_143LYSLYSLYSLYSAA243253
d_144THRTHRPROPROAA249 - 255259 - 265
d_145LEULEULEULEUAA260270
d_146LEULEUGLUGLUAA263 - 264273 - 274
d_147LEULEULEULEUAA286296
d_148LEULEUGLYGLYAA288 - 295298 - 305
d_149TYRTYRASPASPAA297 - 298307 - 308
d_150SERSERGLYGLYAA301 - 304311 - 314
d_151GLYGLYVALVALAA307 - 311317 - 321
d_152SERSERSERSERAA313323
d_153GLYGLYALAALAAA315 - 316325 - 326
d_154LEULEULEULEUAA318328
d_155VALVALVALVALAA321331
d_156PROPROLEULEUAA326 - 327336 - 337
d_157LEULEUSERSERAA329 - 330339 - 340
d_158ALAALATRPTRPAA332 - 340342 - 350
d_159VALVALVALVALAA364374
d_160PHEPHEPHEPHEAA366376
d_161PROPROPHEPHEAA369 - 372379 - 382
d_162GLUGLUGLUGLUAA376386
d_163LYSLYSLYSLYSAA380390
d_164PROPROPROPROAA382392
d_165METMETTHRTHRAA385 - 392395 - 402
d_21ASNASNLYSLYSBB24 - 2534 - 35
d_22PROPROPROPROBB2838
d_23LEULEUPHEPHEBB30 - 3540 - 45
d_24LEULEUTYRTYRBB37 - 3847 - 48
d_25ALAALAALAALABB4252
d_26ILEILEPROPROBB50 - 5460 - 64
d_27ILEILEALAALABB57 - 6267 - 72
d_28LEULEUTHRTHRBB64 - 6874 - 78
d_29ALAALAALAALABB7080
d_210THRTHRASPASPBB72 - 7482 - 84
d_211ILEILEGLYGLYBB76 - 7986 - 89
d_212GLUGLUGLUGLUBB8696
d_213ALAALAGLNGLNBB90 - 91100 - 101
d_214HISHISGLNGLNBB93 - 97103 - 107
d_215LEULEULEULEUBB100110
d_216THRTHRTHRTHRBB114124
d_217GLYGLYGLYGLYBB117127
d_218PHEPHESERSERBB119 - 121129 - 131
d_219LEULEULEULEUBB124134
d_220LYSLYSLEULEUBB129 - 131139 - 141
d_221TYRTYRTYRTYRBB138148
d_222ALAALAALAALABB142152
d_223THRTHRVALVALBB144 - 145154 - 155
d_224PHEPHEPHEPHEBB147157
d_225ILEILEILEILEBB157167
d_226VALVALVALVALBB161171
d_227GLYGLYGLYGLYBB164174
d_228GLNGLNILEILEBB166 - 169176 - 179
d_229ARGARGTHRTHRBB178 - 180188 - 190
d_230PHEPHEALAALABB182 - 183192 - 193
d_231VALVALPHEPHEBB185 - 190195 - 200
d_232LYSLYSGLUGLUBB193 - 195203 - 205
d_233PROPROPROPROBB197207
d_234THRTHRTHRTHRBB203213
d_235GLUGLUHISHISBB206 - 209216 - 219
d_236THRTHRTHRTHRBB214224
d_237VALVALMETMETBB216 - 221226 - 231
d_238GLYGLYMETMETBB225 - 226235 - 236
d_239ASNASNASNASNBB228238
d_240SERSERSERSERBB236 - 237246 - 247
d_241VALVALVALVALBB239249
d_242LEULEULEULEUBB241251
d_243LYSLYSLYSLYSBB243253
d_244THRTHRPROPROBB249 - 255259 - 265
d_245LEULEULEULEUBB260270
d_246LEULEUGLUGLUBB263 - 264273 - 274
d_247LEULEULEULEUBB286296
d_248LEULEUGLYGLYBB288 - 295298 - 305
d_249TYRTYRASPASPBB297 - 298307 - 308
d_250SERSERGLYGLYBB301 - 304311 - 314
d_251GLYGLYVALVALBB307 - 311317 - 321
d_252SERSERSERSERBB313323
d_253GLYGLYALAALABB315 - 316325 - 326
d_254LEULEULEULEUBB318328
d_255VALVALVALVALBB321331
d_256PROPROLEULEUBB326 - 327336 - 337
d_257LEULEUSERSERBB329 - 330339 - 340
d_258ALAALATRPTRPBB332 - 340342 - 350
d_259VALVALVALVALBB364374
d_260PHEPHEPHEPHEBB366376
d_261PROPROPHEPHEBB369 - 372379 - 382
d_262GLUGLUGLUGLUBB376386
d_263LYSLYSLYSLYSBB380390
d_264PROPROPROPROBB382392
d_265METMETTHRTHRBB385 - 392395 - 402

-
Components

#1: Protein Alpha-1-antitrypsin


Mass: 45684.797 Da / Num. of mol.: 2 / Mutation: I340W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1 / Plasmid: pQE30 / Details (production host): T5 promoter / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue / References: UniProt: P01009
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.59 % / Description: Dipyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 0.1M SPG (succinate-phosphate-glycine) pH 5.25, 17.5% PEG1500

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2018 / Details: Compound refractive lenses
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.878→98.251 Å / Num. obs: 19154 / % possible obs: 81.2 % / Redundancy: 10.7 % / Biso Wilson estimate: 69.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.067 / Rrim(I) all: 0.223 / Net I/σ(I): 9.8
Reflection shellResolution: 2.878→3.071 Å / Redundancy: 12.1 % / Rmerge(I) obs: 2.298 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 958 / CC1/2: 0.42 / Rpim(I) all: 0.684 / Rrim(I) all: 2.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
STARANISO2.3.94data scaling
Aimless0.7.13data scaling
XDS20180808data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→98.25 Å / SU ML: 0.4098 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2422 876 4.57 %
Rwork0.1974 18272 -
obs0.1994 19148 81.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.35 Å2
Refinement stepCycle: LAST / Resolution: 2.88→98.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 0 10 5422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225545
X-RAY DIFFRACTIONf_angle_d0.46927561
X-RAY DIFFRACTIONf_chiral_restr0.0402909
X-RAY DIFFRACTIONf_plane_restr0.0033962
X-RAY DIFFRACTIONf_dihedral_angle_d13.90381885
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.332016348911 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.060.4202470.32767X-RAY DIFFRACTION20.97
3.06-3.290.33371530.28943137X-RAY DIFFRACTION85.41
3.29-3.630.30851340.24643353X-RAY DIFFRACTION89.27
3.63-4.150.26081830.19553347X-RAY DIFFRACTION90.89
4.15-5.230.19541730.16133771X-RAY DIFFRACTION99.65
5.23-98.250.21331860.183897X-RAY DIFFRACTION99.61
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)
14.15855540835-0.7320481727622.545178223786.198231305221.746797763458.40234675523-0.2200042156630.109675809564-0.7267337015750.2631144767970.474250308692-0.0057454520313-0.03007797900140.3197185163180.03790027381140.2939749027570.03219544338470.02728985711520.4067048532960.04616302241450.482058599749-30.4325035033-35.5271585827-1.72167761648
21.56030283309-0.3584664387811.124855975642.80987005416-0.3849684248215.92759126820.09439663434150.0234446146572-0.366653877089-0.147881038009-0.194988566120.814427077412-0.00431635617284-0.7587028413160.005033915386210.3262753436310.00363934596726-0.1410070014430.547155760235-0.03251918386530.785639788856-45.309507924-29.690138432-6.64366342081
33.26642367631-0.393123661385-1.912594838755.681751032511.069481277083.37751786238-0.10724170748-0.485765117409-0.07299676904130.7285989520260.1955697766620.1838829403770.06738213039740.0023858908545-0.09325615956850.330921734162-0.0129679350772-0.05691018952430.3814794355110.1157807577090.324849073072-30.5898323331-28.598526219919.8970370077
41.88556043142-0.08055769458420.8163726889991.672093873530.6668352984916.005855144820.1901988934610.0339009001477-0.251530023641-0.0606201702429-0.1055329920270.1840144266590.1357419092350.0728986303418-0.1850043963580.243105011832-0.0582661782859-0.06964520710240.2737116107620.04178887713130.548122327824-33.5899834473-30.54056482540.287316393385
54.825361595551.20603424755-0.7419412261573.469714045410.946683195327.23424462994-0.0351523006677-0.681203207-0.3864986975750.481166272308-0.1021482654840.3733732787350.413061890919-0.918004691810.0888608262220.415485136491-0.029362111204-0.0335641095130.5546793683830.1560619777470.422795476222-35.3309979745-30.615718723318.2105656268
61.84666973824-1.318371636641.776444702523.35486399916-1.321630847042.78643076527-0.02731596287430.3206237321250.274364696707-0.709784329935-0.108436435514-0.0251349476402-1.09615599361-0.9520556817140.02718244964151.138975469630.0975125503963-0.1459065990550.4824891327770.03426080477130.585068978531-29.09276052322.16080022698-11.3103420814
71.54194272760.01632511526361.462155248860.002142139990140.02707956378793.04100080468-0.1092665647450.09662160365050.564561128661-0.589774182807-0.326938149710.236116878706-1.07464807886-0.304833299966-0.4326178574662.393514073190.756335580195-0.5771637936680.5603285365450.2336863284320.741738010509-35.20407736595.54259153775-24.7849094918
81.03322926983-1.96877221023-0.2220900227183.733919358450.6040652927835.622749087210.02578792052460.1255875376920.650322818543-1.10792269290.38361538803-0.95727266882-1.652566358061.148580598570.1596446823661.4644768241-0.2058803049060.3236818062260.744750245120.08502146065580.672055505589-16.20704735823.78937971128-19.3268962115
93.50021233418-0.6553774340960.2663538110333.865476572050.6826403754987.78916833619-0.0105645717730.4116752482890.157190879556-2.22540811172-0.0951445204428-0.0372158818638-1.069096794990.574303851151-0.1807404009181.400358071510.04732768252090.03595205654030.67722513272-0.009275890171890.658718938958-19.5477639681-8.39613581921-30.0580278331
101.38901126023-0.1126709631870.3370276726563.239368188452.693376093493.320362953460.04487276081850.01895131712530.24373996332-0.7565521423830.4591793738-0.417347719656-1.007041286320.520324202181-0.4977610094180.66896661896-0.1348928157760.1460607263120.4162676255010.03396007579340.55143258571-18.1576333824-1.06188495486-0.539155081414
112.25799681666-0.4155394770581.271726691773.048708900660.3435787093292.828938783820.260034155254-0.2260175425121.02474785938-0.952725351189-0.1780720558580.0251058005205-1.39146598553-0.5787953402840.01564212704831.15143403730.0734112910350.1658214156170.510080511082-0.06534082076750.718346204274-26.357166293512.35770836164.96057522847
122.21099990195-0.3261263903580.438327099952.504598884441.404515125884.97542907930.1490999925970.271798685398-0.161622709044-0.918597867214-0.2696759823470.278715050133-0.419675933765-0.9059475934080.2366097077321.236156443610.0590053362688-0.03531578107080.4355292471130.0645896545830.5900296946-31.5075898487-6.81396612907-19.1699814754
131.76097271018-0.906673639155-1.019537834120.8439380101440.6546933123452.51126957870.12016508383-0.2934544793920.230478057979-0.883500894150.22217862463-0.538130947428-0.7837064844450.506508133881-0.1981101958610.812000730853-0.1041952990820.173640579040.485757758260.01233807715750.538602221619-17.45037615351.12381903552-2.38826796543
144.241255852290.9982015195840.3459176861557.43515656295-2.667941139493.136444874610.2765353236380.3412599810810.100304148547-1.58289938340.416682403115-0.6742492183630.5307761423620.7294489846-0.4950152253160.887289880863-0.05605852083080.1232807681330.372744103109-0.06678627683670.514367493624-22.19159114954.266784905832.18671392636
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 44 )AA24 - 441 - 21
22chain 'A' and (resid 45 through 199 )AA45 - 19922 - 173
33chain 'A' and (resid 200 through 255 )AA200 - 255174 - 229
44chain 'A' and (resid 256 through 340 )AA256 - 340230 - 314
55chain 'A' and (resid 341 through 393 )AA341 - 393315 - 365
66chain 'B' and (resid 24 through 67 )BB24 - 671 - 44
77chain 'B' and (resid 68 through 88 )BB68 - 8845 - 65
88chain 'B' and (resid 89 through 121 )BB89 - 12166 - 98
99chain 'B' and (resid 122 through 149 )BB122 - 14999 - 126
1010chain 'B' and (resid 150 through 255 )BB150 - 255127 - 232
1111chain 'B' and (resid 256 through 290 )BB256 - 290233 - 267
1212chain 'B' and (resid 291 through 325 )BB291 - 325268 - 302
1313chain 'B' and (resid 326 through 361 )BB326 - 361303 - 330
1414chain 'B' and (resid 362 through 394 )BB362 - 394331 - 363

+
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