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- PDB-5o3u: Structural characterization of the fast and promiscuous macrocycl... -

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Basic information

Entry
Database: PDB / ID: 5o3u
TitleStructural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin F1
Components
  • Peptide cyclase 1
  • Putative presegetalin F1
KeywordsHYDROLASE / segetalin biosynthesis / prolyl oligopeptidase / macrocyclase / peptidase / beta-propeller / closed form
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative presegetalin F1 / Prolyl endopeptidase
Similarity search - Component
Biological speciesVaccaria hispanica (bladder-soapwort)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLudewig, H. / Czekster, C.M. / Bent, A.F. / Naismith, J.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council339367 NCB-TNT United Kingdom
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Characterization of the Fast and Promiscuous Macrocyclase from Plant PCY1 Enables the Use of Simple Substrates.
Authors: Ludewig, H. / Czekster, C.M. / Oueis, E. / Munday, E.S. / Arshad, M. / Synowsky, S.A. / Bent, A.F. / Naismith, J.H.
History
DepositionMay 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Nov 27, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide cyclase 1
B: Peptide cyclase 1
C: Peptide cyclase 1
D: Peptide cyclase 1
L: Putative presegetalin F1
M: Putative presegetalin F1
N: Putative presegetalin F1
O: Putative presegetalin F1


Theoretical massNumber of molelcules
Total (without water)345,9318
Polymers345,9318
Non-polymers00
Water16,754930
1
A: Peptide cyclase 1
L: Putative presegetalin F1


Theoretical massNumber of molelcules
Total (without water)86,4832
Polymers86,4832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-11 kcal/mol
Surface area28460 Å2
MethodPISA
2
B: Peptide cyclase 1
M: Putative presegetalin F1


Theoretical massNumber of molelcules
Total (without water)86,4832
Polymers86,4832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-10 kcal/mol
Surface area28260 Å2
MethodPISA
3
C: Peptide cyclase 1
N: Putative presegetalin F1


Theoretical massNumber of molelcules
Total (without water)86,4832
Polymers86,4832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-12 kcal/mol
Surface area28150 Å2
MethodPISA
4
D: Peptide cyclase 1
O: Putative presegetalin F1


Theoretical massNumber of molelcules
Total (without water)86,4832
Polymers86,4832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-12 kcal/mol
Surface area28150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.860, 85.820, 137.870
Angle α, β, γ (deg.)87.64, 78.32, 89.52
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17L
27M
18L
28N
19L
29O
110M
210N
111M
211O
112N
212O

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 724
2010B5 - 724
1020A5 - 723
2020C5 - 723
1030A2 - 724
2030D2 - 724
1040B5 - 724
2040C5 - 724
1050B5 - 724
2050D5 - 724
1060C5 - 723
2060D5 - 723
1070L1 - 25
2070M1 - 25
1080L1 - 25
2080N1 - 25
1090L1 - 25
2090O1 - 25
10100M1 - 25
20100N1 - 25
10110M1 - 25
20110O1 - 25
10120N1 - 25
20120O1 - 25

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Peptide cyclase 1


Mass: 82483.266 Da / Num. of mol.: 4 / Mutation: S562A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Gene: Pcy1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4P353
#2: Protein/peptide
Putative presegetalin F1


Mass: 3999.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6LNM3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 930 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: PCY1-S562A complex with PresegF1 was crystallized at 13.0 mg/mL with 0.161.3 mM PresegB1 in 27% (w/v) PEG 3350, 100 mM Ca chloride and 0.1 M Bis-Tris at pH 6.5. For cryo protection 10 % (v/v) ...Details: PCY1-S562A complex with PresegF1 was crystallized at 13.0 mg/mL with 0.161.3 mM PresegB1 in 27% (w/v) PEG 3350, 100 mM Ca chloride and 0.1 M Bis-Tris at pH 6.5. For cryo protection 10 % (v/v) glycerol were added to reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.86→73.72 Å / Num. obs: 222236 / % possible obs: 95.8 % / Redundancy: 3.4 % / Net I/σ(I): 7.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo PCY1

Resolution: 1.86→73.72 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.593 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22338 11725 5 %RANDOM
Rwork0.19295 ---
obs0.19445 222236 95.75 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 27.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20.79 Å20.63 Å2
2--0.27 Å2-0.75 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.86→73.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23233 0 0 930 24163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01923977
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221720
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.95132513
X-RAY DIFFRACTIONr_angle_other_deg0.938350487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33352920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17723.9751185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.381153993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.86515147
X-RAY DIFFRACTIONr_chiral_restr0.0910.23448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02126843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025128
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8891.0111635
X-RAY DIFFRACTIONr_mcbond_other1.8881.0111634
X-RAY DIFFRACTIONr_mcangle_it2.8151.50214522
X-RAY DIFFRACTIONr_mcangle_other2.8151.50214523
X-RAY DIFFRACTIONr_scbond_it3.3371.38612342
X-RAY DIFFRACTIONr_scbond_other3.3371.38612342
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9881.93717975
X-RAY DIFFRACTIONr_long_range_B_refined6.67812.53126160
X-RAY DIFFRACTIONr_long_range_B_other6.68212.39426014
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A469240.07
12B469240.07
21A468820.07
22C468820.07
31A474880.06
32D474880.06
41B472180.07
42C472180.07
51B469980.06
52D469980.06
61C473140.07
62D473140.07
71L6580.05
72M6580.05
81L6540.01
82N6540.01
91L6580.04
92O6580.04
101M6540.01
102N6540.01
111M7020.05
112O7020.05
121N6580.01
122O6580.01
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 851 -
Rwork0.325 16211 -
obs--94.44 %
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)
12.0712-0.4477-0.75421.16150.16091.341-0.00310.24750.1256-0.0742-0.0419-0.0772-0.10270.12020.0450.25-0.0861-0.05640.12760.06080.039513.785-43.145284.314
22.2613-0.76382.56690.7805-1.13344.850.027-0.07050.07450.0217-0.0487-0.0065-0.07370.05810.02180.1526-0.0348-0.03660.03230.0180.05154.192-38.01321.318
31.137-0.0385-0.30953.32631.05631.17880.03460.088-0.0531-0.10380.0298-0.2302-0.0070.133-0.06440.1588-0.022-0.0490.11340.03260.067624.89-50.526325.762
41.6924-1.00130.98821.3746-0.46451.1005-0.0034-0.2131-0.1050.07180.10560.12690.0427-0.1671-0.10220.209-0.0483-0.03770.09250.07350.07131.574-62.636325.355
51.08180.0506-0.16880.8101-0.0610.99450.00220.03330.012-0.0120.01260.03690.00130.0326-0.01480.186-0.0393-0.05860.02810.02620.03074.234-57.336294.592
61.1602-0.1629-0.25061.92381.59463.1477-0.04310.06090.04070.02450.0782-0.0327-0.07450.1614-0.03510.2091-0.0293-0.0490.05140.05010.06721.656-41.443292.553
71.8927-0.59371.0432.14430.37981.66950.2090.4145-0.2876-0.2525-0.29280.2535-0.0549-0.10120.08390.28020.0158-0.11870.2376-0.09270.1405-26.735-16.747285.616
82.1737-0.7597-2.62650.76240.65964.7265-0.0279-0.0713-0.15010.0955-0.00350.07730.051-0.05910.03150.1579-0.0312-0.02960.05150.0590.0819-15.183-25.022321.888
91.1962-0.17590.27233.7389-0.49630.8222-0.05690.0216-0.0622-0.09360.00670.16070.049-0.06650.05020.1402-0.03-0.0090.11170.03970.074-35.688-15.066326.939
102.3111-0.6981-1.00921.35050.0391.8659-0.0424-0.22150.11340.08270.0989-0.0505-0.01060.1587-0.05650.1863-0.0374-0.06550.05990.00680.0281-20.412.394329.473
111.042-0.25080.12532.1927-1.08891.6428-0.0284-0.2260.01370.18490.0686-0.1739-0.06310.1427-0.04020.1931-0.0453-0.050.12120.0220.0933-2.238-6.11316.151
121.1654-0.23060.02061.05940.2230.64640.04070.0713-0.0381-0.091-0.0448-0.0244-0.0104-0.00990.0040.1916-0.0332-0.04620.04410.03230.0333-16.825-6.303295.566
133.02190.2223-1.18281.65090.23311.65450.0391-0.44820.24480.1703-0.05650.0996-0.1614-0.15650.01740.3220.0376-0.03040.2111-0.0190.07791.939-27.985400.799
142.46950.57652.47110.6240.64964.05450.00830.08260.12220.00890.00050.0859-0.0945-0.0447-0.00880.179-0.022-0.01690.04640.06240.101812.484-20.463363.89
150.7585-0.3309-0.12133.9191-0.41960.8585-0.0043-0.042-0.00320.1378-0.00140.2411-0.0527-0.12520.00580.1529-0.0232-0.02380.11630.04640.1226-8.879-31.812358.762
160.46140.00110.42030.24070.02480.91810.0020.12360.0028-0.00020.0193-0.0436-0.02220.1477-0.02130.1901-0.0297-0.03480.07630.03460.046516.548-44.943368.957
171.92440.2960.32171.54850.32521.6279-0.0407-0.09360.04630.13720.01590.072-0.1287-0.14450.02480.2380.0023-0.01150.06480.02770.02194.639-37.916394.838
182.3111-1.58641.30452.7285-2.99565.28370.0532-0.0651-0.046-0.01470.1310.02640.0812-0.065-0.18420.2718-0.0435-0.00030.0183-0.00430.10220.829-26.348389.104
192.39870.26650.85831.40280.35091.7539-0.0092-0.4122-0.18550.1479-0.0004-0.16380.29350.37050.00960.43180.1269-0.01930.29810.07190.0705-21.86-2.606401.77
202.32320.5471-2.56421.1258-0.64774.5399-0.03860.0808-0.05750.05090.00910.05130.09550.0020.02950.1682-0.0273-0.02920.02360.02050.0462-32.812-7.062364.724
211.317-0.0529-0.27943.68490.54651.27520.0185-0.17010.1680.12020.1092-0.29010.01490.2277-0.12770.1425-0.0432-0.0310.1387-0.02760.117-11.7715.288360.412
222.52320.417-1.72630.69180.1793.04230.28560.16460.3661-0.05010.09060.0767-0.2952-0.2749-0.37620.22110.00060.03230.06410.08740.1703-31.15922.185361.133
234.15341.5086-3.54192.235-1.99977.33260.03940.61540.3483-0.29930.17870.3481-0.1007-0.3788-0.21810.2041-0.0252-0.04160.18830.05490.1358-44.4226.824361.048
240.7096-0.1953-0.36871.10740.28791.3756-0.0817-0.15920.0180.11390.1336-0.06690.16490.2301-0.05190.24310.0043-0.04490.11030.01740.0302-32.8629.204392.011
250.0102-0.0603-0.19080.76532.841211.8917-0.04030.00930.00130.0485-0.02360.1271-0.24390.15960.0640.2944-0.030.04380.21970.00220.273211.931-52.212311.576
2614.24593.55066.8554.87263.24577.54260.07040.24820.0285-0.074-0.10180.25460.40470.24350.03140.1932-0.0037-0.0170.08590.01460.12140.555-42.056310.912
270.04890.205-0.65090.9046-2.879110.29380.0105-0.0274-0.0316-0.0342-0.0414-0.15850.33180.03050.03090.278-0.0395-0.05020.24770.01520.2371-23.934-9.978313.646
289.1557-0.2167-4.03113.74230.77935.16890.13450.26280.32750.0273-0.13340.0409-0.288-0.3611-0.00110.1972-0.012-0.0260.09940.0320.1805-12.562-18.968312.663
290.2024-0.7041.85482.5799-6.457219.77190.0410.02460.0512-0.02260.0514-0.1678-0.2940.1466-0.09240.38970.01730.06770.33350.0190.33673.607-35.366372.542
3010.1221-3.4688.72213.9014-3.082115.80580.0411-0.2314-0.37720.24680.0236-0.01340.0848-0.2096-0.06470.2247-0.0340.01880.07490.0550.157316.105-25.821373.898
310.4533-0.048-1.20691.79883.903411.1992-0.0225-0.01850.0404-0.05990.02960.06610.0240.0862-0.00720.28660.0255-0.05470.22020.01480.215-24.2977.153374.565
3212.2719-3.0190.43438.99712.62394.2175-0.0195-0.30120.80160.36460.1193-0.1085-0.25490.2392-0.09980.4017-0.11280.0360.1985-0.06330.1365-35.222-2.154374.655
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 68
2X-RAY DIFFRACTION2A69 - 152
3X-RAY DIFFRACTION3A153 - 296
4X-RAY DIFFRACTION4A297 - 436
5X-RAY DIFFRACTION5A437 - 676
6X-RAY DIFFRACTION6A677 - 724
7X-RAY DIFFRACTION7B8 - 68
8X-RAY DIFFRACTION8B69 - 152
9X-RAY DIFFRACTION9B153 - 277
10X-RAY DIFFRACTION10B278 - 401
11X-RAY DIFFRACTION11B402 - 465
12X-RAY DIFFRACTION12B466 - 724
13X-RAY DIFFRACTION13C5 - 68
14X-RAY DIFFRACTION14C69 - 152
15X-RAY DIFFRACTION15C153 - 297
16X-RAY DIFFRACTION16C298 - 551
17X-RAY DIFFRACTION17C552 - 697
18X-RAY DIFFRACTION18C698 - 724
19X-RAY DIFFRACTION19D4 - 68
20X-RAY DIFFRACTION20D69 - 152
21X-RAY DIFFRACTION21D153 - 296
22X-RAY DIFFRACTION22D297 - 397
23X-RAY DIFFRACTION23D398 - 436
24X-RAY DIFFRACTION24D437 - 724
25X-RAY DIFFRACTION25L1 - 12
26X-RAY DIFFRACTION26L20 - 25
27X-RAY DIFFRACTION27M1 - 11
28X-RAY DIFFRACTION28M19 - 25
29X-RAY DIFFRACTION29N1 - 11
30X-RAY DIFFRACTION30N20 - 25
31X-RAY DIFFRACTION31O1 - 11
32X-RAY DIFFRACTION32O19 - 25

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