[English] 日本語
Yorodumi
- PDB-7k64: Binary titrated soak structure of alkanesulfonate monooxygenase M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k64
TitleBinary titrated soak structure of alkanesulfonate monooxygenase MsuD from Pseudomonas fluorescens with FMN
ComponentsAlkanesulfonate monooxygenase
KeywordsFLAVOPROTEIN / TIM barrel / Flavin-dependent monooxygenase
Function / homology
Function and homology information


alkanesulfonate monooxygenase / alkanesulfonate monooxygenase activity / alkanesulfonate catabolic process / nucleotide binding
Similarity search - Function
Alkanesulphonate monooxygenase, FMN-dependent / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / SUCCINIC ACID / Alkanesulfonate monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLiew, J.J.M. / Dowling, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1807480 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structures of the alkanesulfonate monooxygenase MsuD provide insight into C-S bond cleavage, substrate scope, and an unexpected role for the tetramer.
Authors: Liew, J.J.M. / El Saudi, I.M. / Nguyen, S.V. / Wicht, D.K. / Dowling, D.P.
History
DepositionSep 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 7, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alkanesulfonate monooxygenase
B: Alkanesulfonate monooxygenase
C: Alkanesulfonate monooxygenase
D: Alkanesulfonate monooxygenase
E: Alkanesulfonate monooxygenase
F: Alkanesulfonate monooxygenase
G: Alkanesulfonate monooxygenase
H: Alkanesulfonate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,75623
Polymers354,2318
Non-polymers3,52515
Water73941
1
A: Alkanesulfonate monooxygenase
B: Alkanesulfonate monooxygenase
C: Alkanesulfonate monooxygenase
D: Alkanesulfonate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,81610
Polymers177,1164
Non-polymers1,7006
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Alkanesulfonate monooxygenase
F: Alkanesulfonate monooxygenase
G: Alkanesulfonate monooxygenase
H: Alkanesulfonate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,94013
Polymers177,1164
Non-polymers1,8259
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.010, 212.010, 94.460
Angle α, β, γ (deg.)90.000, 118.848, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 76 or resid 78...
d_2ens_1(chain "B" and (resid 0 through 76 or resid 78...
d_3ens_1(chain "C" and (resid 0 through 76 or resid 78...
d_4ens_1(chain "D" and (resid 0 through 76 or resid 78...
d_5ens_1(chain "E" and (resid 0 through 76 or resid 78...
d_6ens_1(chain "F" and (resid 0 through 76 or resid 78...
d_7ens_1(chain "G" and (resid 0 through 76 or resid 78...
d_8ens_1(chain "H" and (resid 0 through 76 or resid 78...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERILEA1 - 77
d_12ens_1PROGLYA81 - 146
d_13ens_1ALALEUA150 - 231
d_14ens_1VALHISA233 - 252
d_15ens_1LEUARGA287 - 301
d_16ens_1SERLYSA304 - 320
d_17ens_1TYRALAA322 - 360
d_21ens_1SERILED1 - 77
d_22ens_1PROGLYD79 - 144
d_23ens_1ALALEUD146 - 227
d_24ens_1VALHISD231 - 250
d_25ens_1LEUARGD252 - 266
d_26ens_1SERLYSD269 - 285
d_27ens_1TYRALAD287 - 325
d_31ens_1SERILEF1 - 77
d_32ens_1PROGLYF79 - 144
d_33ens_1ALALEUF146 - 227
d_34ens_1VALHISF229 - 248
d_35ens_1LEUARGF283 - 297
d_36ens_1SERLYSF300 - 316
d_37ens_1TYRALAF318 - 356
d_41ens_1SERILEI1 - 77
d_42ens_1PROGLYI81 - 146
d_43ens_1ALALEUI148 - 229
d_44ens_1VALHISI231 - 250
d_45ens_1LEUARGI252 - 266
d_46ens_1SERLYSI269 - 285
d_47ens_1TYRALAI287 - 325
d_51ens_1SERILEK1 - 77
d_52ens_1PROGLYK81 - 146
d_53ens_1ALALEUK148 - 229
d_54ens_1VALHISK231 - 250
d_55ens_1LEUARGK285 - 299
d_56ens_1SERLYSK302 - 318
d_57ens_1TYRALAK320 - 358
d_61ens_1SERILEP1 - 77
d_62ens_1PROGLYP79 - 144
d_63ens_1ALALEUP146 - 227
d_64ens_1VALHISP229 - 248
d_65ens_1LEULYSP250 - 281
d_66ens_1TYRALAP283 - 321
d_71ens_1SERILES1 - 77
d_72ens_1PROGLYS79 - 144
d_73ens_1ALALEUS146 - 227
d_74ens_1VALHISS229 - 248
d_75ens_1LEUARGS253 - 267
d_76ens_1SERLYSS270 - 286
d_77ens_1TYRALAS288 - 326
d_81ens_1SERILEV1 - 77
d_82ens_1PROGLYV79 - 144
d_83ens_1ALALEUV146 - 227
d_84ens_1VALHISV229 - 248
d_85ens_1LEUARGV253 - 267
d_86ens_1SERLYSV270 - 286
d_87ens_1TYRALAV288 - 326

NCS oper:
IDCodeMatrixVector
1given(0.281320483888, -0.175677859551, 0.943396032962), (-0.140401962143, -0.980055412871, -0.14063668344), (0.949287140106, -0.0928906742685, -0.300375179172)-17.4583464958, 2.61549890529, 24.0673277847
2given(-0.97224361857, 0.233914623088, 0.00512788990195), (0.233970130602, 0.971953875414, 0.0237411468633), (0.000569328957331, 0.0242819516055, -0.999704987829)9.63210658655, -1.59114754189, 44.2133432513
3given(-0.298227200029, -0.0584522431139, -0.952703454616), (-0.0587603115764, -0.995105668518, 0.0794476825792), (-0.952684503362, 0.0796746117575, 0.293332905238)27.2747585584, -2.52798309882, 20.2336859529
4given(0.957165756279, 0.10166326796, 0.271105689639), (0.102531570698, -0.994668951788, 0.0109978797264), (0.270778492531, 0.0172700983179, -0.962486754032)-57.170443259, -52.3565728761, -0.565380876964
5given(0.512192597153, -0.295924685335, 0.806279929076), (0.163545078996, 0.955195374655, 0.246687663605), (-0.843155828159, 0.0055115195863, 0.537641025773)-67.060402818, -56.5296357247, -28.2911381099
6given(-0.905648709736, 0.324159300879, -0.273351718865), (-0.328036165662, -0.944097284981, -0.0327504276198), (-0.268686971346, 0.0600088672161, 0.961356462133)-35.9837591171, -49.3908858833, -40.3065038137
7given(-0.555039649688, -0.133750283009, -0.821000517094), (0.0194590354982, 0.98463053982, -0.173562801289), (0.831596256131, -0.112310114633, -0.543906338389)-25.9092198212, -46.8350122856, -12.5931959037

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Alkanesulfonate monooxygenase / FMNH2-dependent aliphatic sulfonate monooxygenase / flavin-dependent methanesulfonate monooxygenase


Mass: 44278.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: msuD, ssuD, Pfl01_3916 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3K9A1, alkanesulfonate monooxygenase

-
Non-polymers , 7 types, 56 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350, sodium succinate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→106.08 Å / Num. obs: 78079 / % possible obs: 97.9 % / Redundancy: 6.19 % / Biso Wilson estimate: 67.079 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.138 / Χ2: 0.913 / Net I/σ(I): 8.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.875.3220.6382.5155610.8670.70794.9
2.87-2.955.650.5143.2655620.90.56796.5
2.95-3.045.5420.4123.9653600.9230.45597.1
3.04-3.135.3220.344.6251730.9360.37695
3.13-3.235.9550.2985.751390.9540.32698.1
3.23-3.356.2010.2576.649750.9660.2898.4
3.35-3.476.2890.2087.8948690.9760.22798.8
3.47-3.616.3590.1749.0346610.9820.18999.1
3.61-3.786.3680.159.8545150.9850.16399.2
3.78-3.966.5240.13310.8142770.9820.14599.4
3.96-4.176.50.12211.5340980.9870.13299.2
4.17-4.436.3810.10911.9738270.9860.11998.7
4.43-4.736.1470.10912.1535760.9840.11896.7
4.73-5.117.0420.10213.1733570.9890.1199.6
5.11-5.67.0030.10213.0531550.9910.1199.3
5.6-6.266.8580.112.9228320.9910.10999.3
6.26-7.236.8960.09813.2324990.9890.10599.2
7.23-8.856.4110.0913.3820950.990.09898.5
8.85-12.527.0250.09114.4816220.9920.09898
12.52-106.086.9570.11714.359260.9760.12797.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K14

7k14


Resolution: 2.8→65.03 Å / SU ML: 0.4479 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Rfree test set was transferred from 7JV3 (unliganded MsuD) due to similar unit cell values
RfactorNum. reflection% reflection
Rfree0.2381 3897 4.99 %
Rwork0.1993 74127 -
obs0.2012 78024 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.78 Å2
Refinement stepCycle: LAST / Resolution: 2.8→65.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21251 0 234 41 21526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001822069
X-RAY DIFFRACTIONf_angle_d0.491230066
X-RAY DIFFRACTIONf_chiral_restr0.05693273
X-RAY DIFFRACTIONf_plane_restr0.0044065
X-RAY DIFFRACTIONf_dihedral_angle_d16.29447932
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.619486626895
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.444713379221
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.597213022439
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.41649051018
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.679155269178
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.561863223326
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.53570848005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.44821460.40772494X-RAY DIFFRACTION93.22
2.83-2.870.47221260.38622602X-RAY DIFFRACTION96.67
2.87-2.910.43941440.36282570X-RAY DIFFRACTION96.34
2.91-2.950.35871310.33752651X-RAY DIFFRACTION97.2
2.95-2.990.35691220.31412580X-RAY DIFFRACTION96.74
2.99-3.030.34851480.29372614X-RAY DIFFRACTION97.6
3.03-3.080.32481340.28742623X-RAY DIFFRACTION97.73
3.08-3.130.34381380.27912509X-RAY DIFFRACTION93.01
3.13-3.190.3131420.27552653X-RAY DIFFRACTION98.35
3.19-3.240.28741260.26362667X-RAY DIFFRACTION98.48
3.24-3.310.29991440.2612616X-RAY DIFFRACTION98.36
3.31-3.370.29141420.25272693X-RAY DIFFRACTION98.88
3.37-3.450.31751330.23932628X-RAY DIFFRACTION99.21
3.45-3.530.28421440.23532694X-RAY DIFFRACTION99.23
3.53-3.620.31651440.22162667X-RAY DIFFRACTION99.4
3.62-3.710.20561400.19372664X-RAY DIFFRACTION99.43
3.71-3.820.23251390.18652690X-RAY DIFFRACTION99.68
3.82-3.950.20891460.17612696X-RAY DIFFRACTION99.54
3.95-4.090.18441460.17272664X-RAY DIFFRACTION99.57
4.09-4.250.20381400.16042677X-RAY DIFFRACTION99.47
4.25-4.440.19821360.1552672X-RAY DIFFRACTION98.98
4.44-4.680.19141390.15472599X-RAY DIFFRACTION96.58
4.68-4.970.17791390.15022717X-RAY DIFFRACTION99.65
4.97-5.350.20331440.15292676X-RAY DIFFRACTION99.79
5.36-5.890.22641400.17532706X-RAY DIFFRACTION99.68
5.89-6.750.19711480.17342702X-RAY DIFFRACTION99.82
6.75-8.50.19861360.16882697X-RAY DIFFRACTION99.54
8.5-65.030.19841400.17952706X-RAY DIFFRACTION98.38
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)
11.52970380238-0.5265144116810.5970942607771.39565520591-0.08679181261141.577984048750.0580227380260.4960782721890.0525886760559-0.0306927253611-0.176642732592-0.2230773649220.002973814841660.5606847770230.09437245988430.415205610049-0.03209152154080.05995279003390.6370341753060.03953929959920.46233782519829.9099599365-12.056979541820.7027655698
22.093532968920.3832624769970.7742690820161.572426758990.6718188777261.761069740880.13920312826-0.2670499421050.1374050440690.284825885899-0.228363257891-0.0457414801768-0.07036034158-0.1517781009310.0743251642530.632765822222-0.1212857534540.01151872294170.4281823663770.01001004910970.4451301880511.38280386078.4925909452944.8787575647
31.847784632910.7531770381130.2042316401361.10300685890.2099119713852.160434878730.0670441617499-0.3313933890960.3143377898680.0425450046386-0.2245905895950.338761051176-0.0903318914158-0.5023218529230.116953314070.480220812423-0.00356602079230.06512946229490.588391075779-0.1268418085930.627736624918-22.1659232591-5.8490607061323.3002625373
42.19991504296-0.8615864143480.994970727421.57674078405-0.5682939219512.041591289340.02628532201820.5864229749110.378509767577-0.160490955141-0.278982802874-0.090785978292-0.2301747112290.3844830059340.1568971002330.612567836269-0.0597394865560.006315200354950.5550290912640.1170650923880.436625919930.85585410965810.1275686505-0.475215587225
50.78486872350.274259795981-0.07321286386851.23920553827-0.03327048785421.34420304310.105738661499-0.1235905355010.02507517032260.176363414418-0.0611551005412-0.180617710360.02206600306840.133269090942-0.04030775164690.471603838284-0.000437343891066-0.05656752096850.448042969961-0.01391400383380.520924559275-24.1192943373-37.0981115782-12.6198270501
62.269854548640.0711595261135-0.3649678323881.331473760470.5419239143061.470390301580.1118662596490.333063547869-0.159016021061-0.239691723535-0.107767182236-0.04321697081450.0656101646952-0.0638164203772-0.004034657488250.5507987025070.0760471877639-0.01800182419820.447404962119-0.02334556636050.548463004613-31.6484536832-58.904559709-40.6164304027
72.22867597431-0.0971404031369-0.2833021237261.2365306205-0.2753427050321.909884395230.1255029546550.35086585927-0.02300896262190.06503651848430.01775027937350.6261327254430.0265535849568-0.593111903152-0.1317476081220.4031327347760.0622369755234-0.002243121215210.6739010415920.02384109740160.893039255576-71.5876390314-47.4435433934-28.3525929333
81.718584924010.553041858509-0.1909778311822.17864077479-0.4615967525671.292606667080.207271689344-0.20865573811-0.003554044304940.410898791059-0.1981728453960.0657254596199-0.0037410519669-0.0600559632496-0.01593042011570.551164377543-0.1129686372480.0429715019040.421322163589-0.005946100132120.397788064206-55.2608951799-62.18072318460.390788462235
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain 'A'AA - C0 - 501
22chain 'B'BD - E0 - 501
33chain 'C'CF - H0 - 501
44chain 'D'DI - J0 - 401
55chain 'E'EK - O0 - 601
66chain 'F'FP - R0 - 601
77chain 'G'GS - U0 - 501
88chain 'H'HV - W0 - 401

+
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