[English] 日本語
Yorodumi
- PDB-6mg6: Crystal structure of carbon-nitrogen hydrolase from Helicobacter ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mg6
TitleCrystal structure of carbon-nitrogen hydrolase from Helicobacter pylori G27
ComponentsCarbon-nitrogen hydrolase
KeywordsHYDROLASE / SSGCID / Structural Genomics / Helicobacter pylori / CN-hydrolase / Carbon-Nitrogen hydrolase / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


: / hydrolase activity
Similarity search - Function
Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Carbon-nitrogen hydrolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of carbon-nitrogen hydrolase from Helicobacter pylori G27
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon-nitrogen hydrolase
B: Carbon-nitrogen hydrolase
C: Carbon-nitrogen hydrolase
D: Carbon-nitrogen hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,5575
Polymers137,4614
Non-polymers961
Water7,080393
1
A: Carbon-nitrogen hydrolase
B: Carbon-nitrogen hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8273
Polymers68,7312
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-37 kcal/mol
Surface area20710 Å2
MethodPISA
2
C: Carbon-nitrogen hydrolase
D: Carbon-nitrogen hydrolase


Theoretical massNumber of molelcules
Total (without water)68,7312
Polymers68,7312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-28 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.580, 91.380, 95.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 0 and (name N or name...
21(chain B and (resid 0 through 16 or (resid 17...
31(chain C and (resid 0 through 16 or (resid 17...
41(chain D and (resid 0 through 31 or (resid 32...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS(chain A and ((resid 0 and (name N or name...AA08
12HISHISILEILE(chain A and ((resid 0 and (name N or name...AA-1 - 2927 - 300
13HISHISILEILE(chain A and ((resid 0 and (name N or name...AA-1 - 2927 - 300
14HISHISILEILE(chain A and ((resid 0 and (name N or name...AA-1 - 2927 - 300
15HISHISILEILE(chain A and ((resid 0 and (name N or name...AA-1 - 2927 - 300
21HISHISLYSLYS(chain B and (resid 0 through 16 or (resid 17...BB0 - 168 - 24
22LYSLYSLYSLYS(chain B and (resid 0 through 16 or (resid 17...BB1725
23HISHISILEILE(chain B and (resid 0 through 16 or (resid 17...BB0 - 2928 - 300
24HISHISILEILE(chain B and (resid 0 through 16 or (resid 17...BB0 - 2928 - 300
25HISHISILEILE(chain B and (resid 0 through 16 or (resid 17...BB0 - 2928 - 300
26HISHISILEILE(chain B and (resid 0 through 16 or (resid 17...BB0 - 2928 - 300
31HISHISLYSLYS(chain C and (resid 0 through 16 or (resid 17...CC0 - 168 - 24
32LYSLYSLYSLYS(chain C and (resid 0 through 16 or (resid 17...CC1725
33HISHISILEILE(chain C and (resid 0 through 16 or (resid 17...CC0 - 2928 - 300
34HISHISILEILE(chain C and (resid 0 through 16 or (resid 17...CC0 - 2928 - 300
35HISHISILEILE(chain C and (resid 0 through 16 or (resid 17...CC0 - 2928 - 300
36HISHISILEILE(chain C and (resid 0 through 16 or (resid 17...CC0 - 2928 - 300
41HISHISLYSLYS(chain D and (resid 0 through 31 or (resid 32...DD0 - 318 - 39
42LYSLYSLYSLYS(chain D and (resid 0 through 31 or (resid 32...DD3240
43HISHISARGARG(chain D and (resid 0 through 31 or (resid 32...DD-3 - 2905 - 298
44HISHISARGARG(chain D and (resid 0 through 31 or (resid 32...DD-3 - 2905 - 298
45HISHISARGARG(chain D and (resid 0 through 31 or (resid 32...DD-3 - 2905 - 298

-
Components

#1: Protein
Carbon-nitrogen hydrolase / HepyC.18002.a.B1


Mass: 34365.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: HPG27_713
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B5Z7B9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic MCSG1 screen, G8: 25% PEG 3350, 200mM Ammonium sulfate, 100mM Tris Base/HCl pH 8.5: HepyC.18002.a.B1.PS38436 at 19.87mg/ml: cryo: 15% EG: tray 3301220G8: puck eko9-11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.1→47.576 Å / Num. obs: 70182 / % possible obs: 99.4 % / Redundancy: 6.543 % / Biso Wilson estimate: 50.265 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Χ2: 0.974 / Net I/σ(I): 25.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.670.5433.3651700.8930.589100
2.15-2.216.4190.444.0450260.9180.479100
2.21-2.286.5270.3515.6945670.9590.38193.8
2.28-2.356.7170.2846.4247730.9660.30899.9
2.35-2.426.4370.2227.9746040.9760.24299.9
2.42-2.516.9050.17610.2744660.9880.191100
2.51-2.66.8540.1511.9643090.9910.16299.8
2.6-2.716.7050.11515.3441500.9940.12599.9
2.71-2.836.3390.09218.2239780.9960.10199.9
2.83-2.976.6630.06824.4138320.9980.07499.8
2.97-3.136.4540.05529.5436330.9980.05999.7
3.13-3.326.5530.0438.8734350.9990.04399.9
3.32-3.556.7220.03147.1932520.9990.03499.7
3.55-3.836.4150.02854.3830300.9990.03199.4
3.83-4.26.1390.02459.5327900.9990.02699.6
4.2-4.76.3890.02165.1255010.02399.6
4.7-5.426.4830.02267.1522550.9990.02499.6
5.42-6.646.4390.02365.5819370.9990.02599.8
6.64-9.395.9950.0268.66153510.02299.7
9.39-47.5765.6790.01770.388900.9990.01998.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
PARROTphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5h8iA as per Morda

Resolution: 2.1→47.576 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 2044 2.91 %0
Rwork0.1679 ---
obs0.169 70175 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.64 Å2 / Biso mean: 55.9961 Å2 / Biso min: 19.53 Å2
Refinement stepCycle: final / Resolution: 2.1→47.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9123 0 5 393 9521
Biso mean--83.13 50.18 -
Num. residues----1172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079379
X-RAY DIFFRACTIONf_angle_d0.84512732
X-RAY DIFFRACTIONf_dihedral_angle_d12.2735483
X-RAY DIFFRACTIONf_chiral_restr0.0581367
X-RAY DIFFRACTIONf_plane_restr0.0061660
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5057X-RAY DIFFRACTION5.504TORSIONAL
12B5057X-RAY DIFFRACTION5.504TORSIONAL
13C5057X-RAY DIFFRACTION5.504TORSIONAL
14D5057X-RAY DIFFRACTION5.504TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.25131610.218944964657100
2.1489-2.20260.2531380.221144964634100
2.2026-2.26220.42371400.33724225436594
2.2622-2.32870.27031340.206244994633100
2.3287-2.40390.23591310.193645094640100
2.4039-2.48980.20641400.176645204660100
2.4898-2.58950.22551350.18345214656100
2.5895-2.70730.26461300.184645564686100
2.7073-2.850.24141350.183845364671100
2.85-3.02860.2191370.185245424679100
3.0286-3.26240.19621420.183845654707100
3.2624-3.59060.2071450.169645554700100
3.5906-4.10990.17881300.1454594472499
4.1099-5.1770.15950.12846804775100
5.177-47.58860.19651510.160648374988100
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)
12.34250.11040.5945.08361.09173.0001-0.1254-0.4818-0.52510.47920.0913-0.10870.21010.07160.03720.36010.06030.04870.41690.19280.43056.610119.49326.3782
22.7975-0.66210.49393.05670.59641.9461-0.1576-0.2856-0.37550.28490.0852-0.4290.1220.25510.08170.25860.02890.0120.36470.12640.376813.720427.759720.0717
32.37350.12260.93553.1679-0.08740.9617-0.1454-0.4702-0.21640.34560.1686-0.02310.0338-0.08410.0240.21680.01230.0310.30720.05850.2489-1.639631.524117.6945
43.58720.0432-2.49572.8933-0.54128.70260.1162-0.9073-0.57780.42930.08020.3005-0.2184-0.2524-0.10380.2856-0.00950.07310.49180.18540.4276-13.927825.977223.0078
52.20990.30260.91231.48990.08853.91850.0022-0.7457-0.44610.53120.05890.08880.1711-0.4392-0.01960.40990.08380.08720.51330.19340.413-4.857423.234327.8687
62.189-0.80940.83370.7398-0.07211.88420.10590.0315-0.4832-0.1856-0.11420.13830.3108-0.0876-0.01750.2411-0.09350.03730.240.02990.3384-11.730425.16675.7614
72.4223-0.20550.71732.31410.24581.95730.1234-0.4825-0.25760.4752-0.06330.74680.5262-0.53150.05030.3394-0.0490.0950.60270.16690.6464-40.140929.719113.7792
82.878-0.04932.0132.54981.36322.67390.2888-0.7054-0.41210.2797-0.04010.98020.5841-1.6341-0.09670.315-0.09080.05160.72380.08870.8735-48.858929.249311.5445
91.91550.37631.31953.05421.7593.6438-0.1981-0.4353-0.5144-0.17380.15530.3934-0.02350.13190.11710.3029-0.0437-0.03030.47630.14620.5989-38.215328.05845.8145
105.8032-2.7634-3.67053.8483.10915.7582-0.1897-0.0594-0.3193-0.2432-0.11030.9041-0.1639-0.55070.39040.3245-0.0295-0.10350.54620.09970.6496-44.633134.3078-1.0317
113.49510.34870.46231.94420.71433.589-0.21530.0266-0.2877-0.19040.14780.39580.0718-0.2230.07470.2681-0.0326-0.04420.26140.07490.3944-32.335934.4959-0.9786
122.25380.58910.65740.49770.24041.8305-0.0997-0.2482-0.46110.13510.14580.31540.2147-0.1607-0.02850.2157-0.02810.0030.22090.05650.3319-25.591232.41598.8966
133.38861.88930.58572.04650.07752.51210.0554-0.3537-0.7335-0.05210.06050.20410.4228-0.2881-0.12150.3118-0.05520.00590.36440.13290.4478-22.07121.536614.439
142.72061.55251.23762.92142.15623.09720.1228-0.2956-0.61320.25990.02130.3350.5486-0.3378-0.15470.3737-0.04710.0160.42570.19590.5897-32.431621.829511.952
153.64344.03560.5234.44870.66021.00260.2348-1.08120.00110.3777-0.320.47820.1362-0.39690.04610.38480.00790.07060.61410.04170.406-26.739237.793624.3881
163.4850.95441.03393.84992.7512.5554-0.1463-0.1645-0.0642-0.01620.2097-0.12220.23360.1603-0.00630.2273-0.0018-0.01190.22150.06150.2525-6.699437.58548.8508
172.09660.4598-0.18792.8081-1.70473.8027-0.02610.617-0.6336-0.6448-0.0731-0.18440.5240.59250.08090.6172-0.01670.03920.6835-0.29530.5602-7.905514.1799-29.0251
182.7973-1.306-1.17243.91830.38545.58550.04190.4995-0.7441-0.25250.1304-0.64080.43590.8823-0.04020.4050.04070.01180.5452-0.21830.615-3.006313.0696-18.0374
191.0425-0.71450.61223.1314-0.8261.948-0.02660.4511-0.2667-0.41210.0609-0.0352-0.02280.1995-0.02370.4057-0.1260.00840.497-0.11580.3472-11.396726.0866-20.9301
206.59171.82872.0285.51532.48624.6980.26850.5512-0.8006-0.4814-0.0519-0.142-0.12240.364-0.25750.7188-0.1089-0.16490.6876-0.0440.4413-24.177428.0538-33.1536
211.708-0.22480.13422.3470.65411.2114-0.09570.5878-0.5122-0.83940.14850.00850.32670.2506-0.11330.6359-0.1395-0.07360.6476-0.17690.4297-18.729319.0537-31.591
223.1717-0.3449-0.41946.6273-0.44262.1772-0.11021.10190.1303-1.446-0.2216-0.5513-0.55250.67740.25971.1289-0.21260.12620.9846-0.04980.4339-7.260432.0227-40.5875
233.9539-0.1902-0.47393.5751-0.33841.85750.20880.58610.4213-0.43760.007-0.4532-0.76690.1769-0.17670.7805-0.1945-0.02320.5310.0260.4716-19.87748.1707-23.5251
241.9905-0.87530.30194.6002-0.38443.54070.44240.87850.2366-0.2513-0.00220.2937-0.5464-0.5457-0.33560.927-0.0866-0.19551.0410.29170.5596-41.867152.0317-41.2926
252.0707-1.38011.22893.3975-1.22783.60.00650.66450.6078-0.55290.0694-0.1005-0.78530.1333-0.08110.9857-0.0472-0.02240.70910.20980.6316-34.744659.857-33.516
262.0631-0.2135-0.47182.0924-1.00413.08730.10510.93330.3366-0.94930.0434-0.08490.1383-0.0142-0.18980.8924-0.1037-0.07790.71480.11160.3808-28.133245.1506-38.2308
272.5628-1.45751.92641.0014-1.19573.8311-0.10710.466-0.1792-0.69560.30530.35150.1284-0.2643-0.2750.6886-0.2066-0.15760.52010.02750.3572-31.396636.1537-26.6673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 55 )A-1 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 114 )A56 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 185 )A115 - 185
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 207 )A186 - 207
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 254 )A208 - 254
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 292 )A255 - 292
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 14 )B0 - 14
8X-RAY DIFFRACTION8chain 'B' and (resid 15 through 32 )B15 - 32
9X-RAY DIFFRACTION9chain 'B' and (resid 33 through 55 )B33 - 55
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 79 )B56 - 79
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 139 )B80 - 139
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 185 )B140 - 185
13X-RAY DIFFRACTION13chain 'B' and (resid 186 through 207 )B186 - 207
14X-RAY DIFFRACTION14chain 'B' and (resid 208 through 254 )B208 - 254
15X-RAY DIFFRACTION15chain 'B' and (resid 255 through 272 )B255 - 272
16X-RAY DIFFRACTION16chain 'B' and (resid 273 through 292 )B273 - 292
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 55 )C0 - 55
18X-RAY DIFFRACTION18chain 'C' and (resid 56 through 79 )C56 - 79
19X-RAY DIFFRACTION19chain 'C' and (resid 80 through 185 )C80 - 185
20X-RAY DIFFRACTION20chain 'C' and (resid 186 through 207 )C186 - 207
21X-RAY DIFFRACTION21chain 'C' and (resid 208 through 254 )C208 - 254
22X-RAY DIFFRACTION22chain 'C' and (resid 255 through 272 )C255 - 272
23X-RAY DIFFRACTION23chain 'C' and (resid 273 through 292 )C273 - 292
24X-RAY DIFFRACTION24chain 'D' and (resid -3 through 55 )D-3 - 55
25X-RAY DIFFRACTION25chain 'D' and (resid 56 through 144 )D56 - 144
26X-RAY DIFFRACTION26chain 'D' and (resid 145 through 240 )D145 - 240
27X-RAY DIFFRACTION27chain 'D' and (resid 241 through 290 )D241 - 290

+
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