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- PDB-1p4a: Crystal Structure of the PurR complexed with cPRPP -

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Basic information

Entry
Database: PDB / ID: 1p4a
TitleCrystal Structure of the PurR complexed with cPRPP
ComponentsPur operon repressor
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


negative regulation of purine nucleobase metabolic process / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Pur operon repressor / Bacterial purine repressor, N-terminal / Bacterial purine repressor, N-terminal / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Pur operon repressor / Bacterial purine repressor, N-terminal / Bacterial purine repressor, N-terminal / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-PCP / Pur operon repressor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsBera, A.K. / Zhu, J. / Zalkin, H. / Smith, J.L.
CitationJournal: J.Bacteriol. / Year: 2003
Title: Functional dissection of the Bacillus subtilis pur operator site.
Authors: Bera, A.K. / Zhu, J. / Zalkin, H. / Smith, J.L.
History
DepositionApr 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_ncs_dom_lim / struct_site
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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pur operon repressor
B: Pur operon repressor
C: Pur operon repressor
D: Pur operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5968
Polymers125,0444
Non-polymers1,5524
Water10,341574
1
A: Pur operon repressor
B: Pur operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2984
Polymers62,5222
Non-polymers7762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-40 kcal/mol
Surface area23610 Å2
MethodPISA
2
C: Pur operon repressor
D: Pur operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2984
Polymers62,5222
Non-polymers7762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-42 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.371, 135.718, 82.071
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D
15A
25B
35C
45D
16A
26B
36C
46D
17A
27B
37C
47D
18A
28B
38C
48D
19A
29B
39C
49D
110A
210B
310C
410D
111A
211B
311C
411D
112A
212B
312C
412D
113A
213B
313C
413D
114A
214B
314C
414D
115A
215B
315C
415D
116A
216B
316C
416D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGTHRTHRAA5 - 185 - 18
21ARGARGTHRTHRBB5 - 185 - 18
31ARGARGTHRTHRCC5 - 185 - 18
41ARGARGTHRTHRDD5 - 185 - 18
12LEULEUTYRTYRAA26 - 3326 - 33
22LEULEUTYRTYRBB26 - 3326 - 33
32LEULEUTYRTYRCC26 - 3326 - 33
42LEULEUTYRTYRDD26 - 3326 - 33
13LYSLYSGLNGLNAA37 - 5337 - 53
23LYSLYSGLNGLNBB37 - 5337 - 53
33LYSLYSGLNGLNCC37 - 5337 - 53
43LYSLYSGLNGLNDD37 - 5337 - 53
14THRTHRTHRTHRAA58 - 6158 - 61
24THRTHRTHRTHRBB58 - 6158 - 61
34THRTHRTHRTHRCC58 - 6158 - 61
44THRTHRTHRTHRDD58 - 6158 - 61
15GLYGLYILEILEAA68 - 7268 - 72
25GLYGLYILEILEBB68 - 7268 - 72
35GLYGLYILEILECC68 - 7268 - 72
45GLYGLYILEILEDD68 - 7268 - 72
16GLNGLNALAALAAA77 - 9277 - 92
26GLNGLNALAALABB77 - 9277 - 92
36GLNGLNALAALACC77 - 9277 - 92
46GLNGLNALAALADD77 - 9277 - 92
17SERSERALAALAAA113 - 127113 - 127
27SERSERALAALABB113 - 127113 - 127
37SERSERALAALACC113 - 127113 - 127
47SERSERALAALADD113 - 127113 - 127
18ASPASPTHRTHRAA132 - 136132 - 136
28ASPASPTHRTHRBB132 - 136132 - 136
38ASPASPTHRTHRCC132 - 136132 - 136
48ASPASPTHRTHRDD132 - 136132 - 136
19GLYGLYLEULEUAA141 - 152141 - 152
29GLYGLYLEULEUBB141 - 152141 - 152
39GLYGLYLEULEUCC141 - 152141 - 152
49GLYGLYLEULEUDD141 - 152141 - 152
110VALVALVALVALAA156 - 159156 - 159
210VALVALVALVALBB156 - 159156 - 159
310VALVALVALVALCC156 - 159156 - 159
410VALVALVALVALDD156 - 159156 - 159
111SERSERTYRTYRAA169 - 175169 - 175
211SERSERTYRTYRBB169 - 175169 - 175
311SERSERTYRTYRCC169 - 175169 - 175
411SERSERTYRTYRDD169 - 175169 - 175
112GLNGLNALAALAAA184 - 189184 - 189
212GLNGLNALAALABB184 - 189184 - 189
312GLNGLNALAALACC184 - 189184 - 189
412GLNGLNALAALADD184 - 189184 - 189
113VALVALLYSLYSAA199 - 207199 - 207
213VALVALLYSLYSBB199 - 207199 - 207
313VALVALLYSLYSCC199 - 207199 - 207
413VALVALLYSLYSDD199 - 207199 - 207
114GLYGLYASPASPAA209 - 220209 - 220
214GLYGLYASPASPBB209 - 220209 - 220
314GLYGLYASPASPCC209 - 220209 - 220
414GLYGLYASPASPDD209 - 220209 - 220
115ALAALAALAALAAA227 - 235227 - 235
215ALAALAALAALABB227 - 235227 - 235
315ALAALAALAALACC227 - 235227 - 235
415ALAALAALAALADD227 - 235227 - 235
116SERSERPHEPHEAA261 - 273261 - 273
216SERSERPHEPHEBB261 - 273261 - 273
316SERSERPHEPHECC261 - 273261 - 273
416SERSERPHEPHEDD261 - 273261 - 273

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16

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Components

#1: Protein
Pur operon repressor


Mass: 31260.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PURR / Production host: Escherichia coli (E. coli) / References: UniProt: P37551
#2: Chemical
ChemComp-PCP / 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE / CARBOXYLIC PRPP / CPRPP


Mass: 388.097 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15O13P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, Sodium chloride, Calcium chloride, Ammonium sulfate, magnesium chloride, cPRPP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMHEPES1droppH8.0
3300 mM1dropNaCl
450 mMammonium sulfate1drop
510 mM1dropMgCl2
65 mMcPRPP1drop
7100 mMHEPES1reservoirpH7.5
8200 mM1reservoirCaCl2
928 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.22→37.8 Å / Num. all: 61803 / Num. obs: 58633 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.22→2.3 Å / % possible all: 92.8
Reflection
*PLUS
Rmerge(I) obs: 0.055
Reflection shell
*PLUS
Rmerge(I) obs: 0.318

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→37.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.284 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23366 3137 5.1 %RANDOM
Rwork0.17731 ---
obs0.18032 58633 98.52 %-
all-61803 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.233 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.02 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.22→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8264 0 88 574 8926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228475
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9911466
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.13251066
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.21359
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026120
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.34277
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.5955
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.3109
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.540
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.78665314
X-RAY DIFFRACTIONr_mcangle_it4.25288590
X-RAY DIFFRACTIONr_scbond_it5.702103161
X-RAY DIFFRACTIONr_scangle_it7.6122876
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A113medium positional0.222.5
12B113medium positional0.282.5
13C113medium positional0.292.5
14D113medium positional0.372.5
21A75medium positional0.242.5
22B75medium positional0.352.5
23C75medium positional0.512.5
24D75medium positional0.22.5
31A137medium positional0.242.5
32B137medium positional0.292.5
33C137medium positional0.252.5
34D137medium positional0.462.5
41A30medium positional0.72.5
42B30medium positional0.622.5
43C30medium positional0.582.5
44D30medium positional0.532.5
51A40medium positional0.312.5
52B40medium positional0.322.5
53C40medium positional0.332.5
54D40medium positional0.42.5
61A120medium positional0.462.5
62B120medium positional0.282.5
63C120medium positional0.312.5
64D120medium positional0.332.5
71A109medium positional0.262.5
72B109medium positional0.272.5
73C109medium positional0.222.5
74D109medium positional0.232.5
81A37medium positional0.172.5
82B37medium positional0.192.5
83C37medium positional0.242.5
84D37medium positional0.252.5
91A85medium positional0.772.5
92B85medium positional0.842.5
93C85medium positional0.692.5
94D85medium positional0.732.5
101A29medium positional0.22.5
102B29medium positional0.442.5
103C29medium positional0.182.5
104D29medium positional0.142.5
111A54medium positional0.72.5
112B54medium positional0.432.5
113C54medium positional0.462.5
114D54medium positional0.42.5
121A43medium positional0.412.5
122B43medium positional0.222.5
123C43medium positional0.242.5
124D43medium positional0.422.5
131A75medium positional0.482.5
132B75medium positional0.272.5
133C75medium positional0.262.5
134D75medium positional0.192.5
141A83medium positional0.292.5
142B83medium positional0.382.5
143C83medium positional0.322.5
144D83medium positional0.252.5
151A57medium positional0.192.5
152B57medium positional0.192.5
153C57medium positional0.152.5
154D57medium positional0.372.5
161A112medium positional0.782.5
162B112medium positional0.582.5
163C112medium positional0.652.5
164D112medium positional0.482.5
11A113medium thermal2.5310
12B113medium thermal2.4510
13C113medium thermal2.7310
14D113medium thermal2.5310
21A75medium thermal2.0710
22B75medium thermal2.3210
23C75medium thermal1.9510
24D75medium thermal2.6110
31A137medium thermal2.6510
32B137medium thermal2.7910
33C137medium thermal2.5610
34D137medium thermal2.5810
41A30medium thermal4.1110
42B30medium thermal4.2910
43C30medium thermal4.6410
44D30medium thermal4.0610
51A40medium thermal2.6610
52B40medium thermal2.9510
53C40medium thermal3.0310
54D40medium thermal2.9110
61A120medium thermal3.0110
62B120medium thermal3.5310
63C120medium thermal2.4610
64D120medium thermal2.8410
71A109medium thermal2.3510
72B109medium thermal2.910
73C109medium thermal2.3610
74D109medium thermal2.4710
81A37medium thermal210
82B37medium thermal2.2810
83C37medium thermal1.7410
84D37medium thermal2.310
91A85medium thermal4.6510
92B85medium thermal2.5410
93C85medium thermal3.6310
94D85medium thermal2.5710
101A29medium thermal2.4310
102B29medium thermal2.3810
103C29medium thermal3.3610
104D29medium thermal2.1710
111A54medium thermal4.2110
112B54medium thermal4.0610
113C54medium thermal4.410
114D54medium thermal3.9310
121A43medium thermal4.9210
122B43medium thermal4.3310
123C43medium thermal5.0910
124D43medium thermal4.2610
131A75medium thermal4.410
132B75medium thermal5.0310
133C75medium thermal2.410
134D75medium thermal2.810
141A83medium thermal4.0710
142B83medium thermal3.8910
143C83medium thermal3.3810
144D83medium thermal3.310
151A57medium thermal3.2210
152B57medium thermal3.7910
153C57medium thermal2.1810
154D57medium thermal1.9910
161A112medium thermal4.3310
162B112medium thermal4.6410
163C112medium thermal3.1510
164D112medium thermal4.9610
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 209
Rwork0.218 4098
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)
11.97060.35190.57251.87950.50431.38730.08290.018-0.0572-0.0882-0.1002-0.11540.2321-0.00170.01730.1450.02790.04440.0746-0.02010.071340.681948.233137.7483
21.28910.4507-0.32971.841-0.3951.19810.0356-0.17180.14620.2565-0.0108-0.2293-0.13510.231-0.02480.0626-0.0401-0.04820.128-0.04230.141647.815873.612657.3695
31.545-0.1794-0.75981.54810.14241.86980.0280.1551-0.0821-0.2494-0.0547-0.0377-0.00260.10830.02670.13490.01420.00050.0963-0.02260.047238.358563.237125.7059
41.5870.1025-0.0151.82240.35811.4574-0.0151-0.10330.04630.06150.00890.1471-0.064-0.07330.00620.00730.02210.00540.08-0.01670.087121.905474.585252.0284
51.9826-0.04930.57141.99350.01442.9386-0.0120.19770.0635-0.1936-0.1185-0.031-0.0634-0.03910.13050.10920.01760.02990.08390.03590.040418.103102.3332-16.928
61.5884-0.32570.09782.1976-1.18492.2036-0.0425-0.1426-0.040.181-0.0157-0.2371-0.02180.17460.05820.08230.0041-0.03610.11450.03390.077929.22190.345911.9785
71.91690.5094-0.39852.12950.0672.02420.0975-0.00160.137-0.0705-0.14240.0352-0.34410.00610.04490.19330.032-0.01910.06310.02330.061415.1647117.4846-5.3746
81.26820.08920.34391.53380.34633.18550.0236-0.0579-0.22450.2268-0.01290.27510.4049-0.4241-0.01070.1415-0.07210.05420.14920.00630.17692.999592.788913.1777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 722 - 72
2X-RAY DIFFRACTION2AA75 - 27675 - 276
3X-RAY DIFFRACTION3BB2 - 722 - 72
4X-RAY DIFFRACTION4BB75 - 27375 - 273
5X-RAY DIFFRACTION5CC2 - 722 - 72
6X-RAY DIFFRACTION6CC75 - 27375 - 273
7X-RAY DIFFRACTION7DD2 - 722 - 72
8X-RAY DIFFRACTION8DD75 - 27375 - 273
Refinement
*PLUS
Rfactor Rfree: 0.234 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: r_bond_d / Dev ideal: 0.009

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