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- PDB-4bmv: Short-chain dehydrogenase from Sphingobium yanoikuyae in complex ... -

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Basic information

Entry
Database: PDB / ID: 4bmv
TitleShort-chain dehydrogenase from Sphingobium yanoikuyae in complex with NADPH
ComponentsSHORT-CHAIN DEHYDROGENASE
KeywordsOXIDOREDUCTASE / BIOCATALYST
Function / homology
Function and homology information


short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain dehydrogenase
Similarity search - Component
Biological speciesSPHINGOBIUM YANOIKUYAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMan, H. / Kedziora, K. / Lavandera-Garcia, I. / Gotor-Fernandez, V. / Grogan, G.
CitationJournal: Top.Catal. / Year: 2014
Title: Structures of Alcohol Dehydrogenases from Ralstonia and Sphingobium Spp. Reveal the Molecular Basis for Their Recognition of 'Bulky-Bulky' Ketones
Authors: Man, H. / Kedziora, K. / Kulig, J. / Frank, A. / Lavandera, I. / Gotor-Fernandez, V. / Rother, D. / Hart, S. / Turkenburg, J.P. / Grogan, G.
History
DepositionMay 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _pdbx_database_status.status_code_sf / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: SHORT-CHAIN DEHYDROGENASE
B: SHORT-CHAIN DEHYDROGENASE
C: SHORT-CHAIN DEHYDROGENASE
D: SHORT-CHAIN DEHYDROGENASE
E: SHORT-CHAIN DEHYDROGENASE
F: SHORT-CHAIN DEHYDROGENASE
G: SHORT-CHAIN DEHYDROGENASE
H: SHORT-CHAIN DEHYDROGENASE
I: SHORT-CHAIN DEHYDROGENASE
J: SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,45220
Polymers279,01810
Non-polymers7,43410
Water5,224290
1
A: SHORT-CHAIN DEHYDROGENASE
B: SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2904
Polymers55,8042
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-65.9 kcal/mol
Surface area22840 Å2
MethodPISA
2
C: SHORT-CHAIN DEHYDROGENASE
D: SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2904
Polymers55,8042
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-69.7 kcal/mol
Surface area22320 Å2
MethodPISA
3
E: SHORT-CHAIN DEHYDROGENASE
F: SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2904
Polymers55,8042
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-67.2 kcal/mol
Surface area22270 Å2
MethodPISA
4
H: SHORT-CHAIN DEHYDROGENASE
I: SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2904
Polymers55,8042
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-45.4 kcal/mol
Surface area22130 Å2
MethodPISA
5
G: SHORT-CHAIN DEHYDROGENASE
J: SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2904
Polymers55,8042
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-55.1 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.910, 86.840, 155.610
Angle α, β, γ (deg.)90.00, 106.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRARGARGAA3 - 2573 - 257
21THRTHRARGARGBB3 - 2573 - 257
12THRTHRARGARGAA3 - 2573 - 257
22THRTHRARGARGCC3 - 2573 - 257
13THRTHRARGARGAA3 - 2573 - 257
23THRTHRARGARGDD3 - 2573 - 257
14THRTHRARGARGAA3 - 2573 - 257
24THRTHRARGARGEE3 - 2573 - 257
15LEULEUARGARGAA4 - 2574 - 257
25LEULEUARGARGFF4 - 2574 - 257
16LEULEUARGARGAA4 - 2574 - 257
26LEULEUARGARGGG4 - 2574 - 257
17LEULEUARGARGAA4 - 2574 - 257
27LEULEUARGARGHH4 - 2574 - 257
18LEULEUTYRTYRAA4 - 2584 - 258
28LEULEUTYRTYRII4 - 2584 - 258
19LEULEUARGARGAA4 - 2574 - 257
29LEULEUARGARGJJ4 - 2574 - 257
110THRTHRTYRTYRBB3 - 2583 - 258
210THRTHRTYRTYRCC3 - 2583 - 258
111THRTHRARGARGBB3 - 2593 - 259
211THRTHRARGARGDD3 - 2593 - 259
112THRTHRARGARGBB3 - 2593 - 259
212THRTHRARGARGEE3 - 2593 - 259
113LEULEUTYRTYRBB4 - 2584 - 258
213LEULEUTYRTYRFF4 - 2584 - 258
114LEULEUTYRTYRBB4 - 2584 - 258
214LEULEUTYRTYRGG4 - 2584 - 258
115LEULEUTYRTYRBB4 - 2584 - 258
215LEULEUTYRTYRHH4 - 2584 - 258
116LEULEUARGARGBB4 - 2574 - 257
216LEULEUARGARGII4 - 2574 - 257
117LEULEUARGARGBB4 - 2594 - 259
217LEULEUARGARGJJ4 - 2594 - 259
118THRTHRTYRTYRCC3 - 2583 - 258
218THRTHRTYRTYRDD3 - 2583 - 258
119THRTHRTYRTYRCC3 - 2583 - 258
219THRTHRTYRTYREE3 - 2583 - 258
120LEULEUTYRTYRCC4 - 2584 - 258
220LEULEUTYRTYRFF4 - 2584 - 258
121LEULEUTYRTYRCC4 - 2584 - 258
221LEULEUTYRTYRGG4 - 2584 - 258
122LEULEUTYRTYRCC4 - 2584 - 258
222LEULEUTYRTYRHH4 - 2584 - 258
123LEULEUARGARGCC4 - 2574 - 257
223LEULEUARGARGII4 - 2574 - 257
124LEULEUTYRTYRCC4 - 2584 - 258
224LEULEUTYRTYRJJ4 - 2584 - 258
125THRTHRARGARGDD3 - 2593 - 259
225THRTHRARGARGEE3 - 2593 - 259
126LEULEUTYRTYRDD4 - 2584 - 258
226LEULEUTYRTYRFF4 - 2584 - 258
127LEULEUTYRTYRDD4 - 2584 - 258
227LEULEUTYRTYRGG4 - 2584 - 258
128LEULEUTYRTYRDD4 - 2584 - 258
228LEULEUTYRTYRHH4 - 2584 - 258
129LEULEUARGARGDD4 - 2574 - 257
229LEULEUARGARGII4 - 2574 - 257
130LEULEUARGARGDD4 - 2594 - 259
230LEULEUARGARGJJ4 - 2594 - 259
131LEULEUTYRTYREE4 - 2584 - 258
231LEULEUTYRTYRFF4 - 2584 - 258
132LEULEUTYRTYREE4 - 2584 - 258
232LEULEUTYRTYRGG4 - 2584 - 258
133LEULEUTYRTYREE4 - 2584 - 258
233LEULEUTYRTYRHH4 - 2584 - 258
134LEULEUARGARGEE4 - 2574 - 257
234LEULEUARGARGII4 - 2574 - 257
135LEULEUARGARGEE4 - 2594 - 259
235LEULEUARGARGJJ4 - 2594 - 259
136LEULEUARGARGFF4 - 2594 - 259
236LEULEUARGARGGG4 - 2594 - 259
137LEULEUARGARGFF4 - 2594 - 259
237LEULEUARGARGHH4 - 2594 - 259
138LEULEUTYRTYRFF4 - 2584 - 258
238LEULEUTYRTYRII4 - 2584 - 258
139LEULEUARGARGFF4 - 2594 - 259
239LEULEUARGARGJJ4 - 2594 - 259
140LEULEUARGARGGG4 - 2594 - 259
240LEULEUARGARGHH4 - 2594 - 259
141LEULEUTYRTYRGG4 - 2584 - 258
241LEULEUTYRTYRII4 - 2584 - 258
142LEULEUARGARGGG4 - 2594 - 259
242LEULEUARGARGJJ4 - 2594 - 259
143LEULEUTYRTYRHH4 - 2584 - 258
243LEULEUTYRTYRII4 - 2584 - 258
144LEULEUARGARGHH4 - 2594 - 259
244LEULEUARGARGJJ4 - 2594 - 259
145LEULEUARGARGII4 - 2574 - 257
245LEULEUARGARGJJ4 - 2574 - 257

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

NCS oper:
IDCodeMatrixVector
1given(-1), (1), (-1)
2given(-1, 0.000422, -0.01564), (-0.000447, -1, 0.01565), (-0.01564, 0.001565, 1)28.74, -0.2205, 0.02745
3given(0.9586, 0.187, 0.2149), (0.1996, 0.09759, -0.975), (-0.2033, 0.9775, 0.05622)11.17, 55.58, 54.97
4given(-0.9622, -0.1767, -0.2073), (-0.1922, -0.09907, 0.9764), (-0.193, 0.9793, 0.06134)16.67, -55.49, 54.8
5given(-0.9585, -0.187, 0.215), (-0.1996, -0.09817, -0.975), (0.2035, -0.9774, 0.05678)38.58, 61.29, 49.01
6given(0.9619, 0.1766, -0.2085), (0.1935, 0.09842, 0.9762), (0.1929, -0.9793, 0.0605)-10.81, -61.11, 49.21
7given(-0.9239, -0.3825, 0.0102), (-0.3798, 0.9136, -0.1453), (0.04624, -0.1381, -0.9893)72.52, 21.81, 107.3
8given(0.9237, 0.3831, 0.001582), (0.3791, -0.9135, -0.1474), (-0.05503, 0.1368, -0.9891)46.32, 10.86, 108.4
9given(-0.9251, -0.3796, -0.003098), (-0.3757, 0.9145, 0.1503), (-0.05423, 0.1402, -0.9886)-17.71, -10.81, 108.4
10given(0.9246, 0.3806, -0.01668), (0.3789, -0.9139, 0.1456), (0.04017, -0.1409, -0.9892)-43.84, -21.75, 107.7

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Components

#1: Protein
SHORT-CHAIN DEHYDROGENASE / / ALCOHOL DEHYDROGENASE


Mass: 27901.842 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPHINGOBIUM YANOIKUYAE (bacteria) / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9U359, alcohol dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1M MES BUFFER PH 5.5 WITH 0.3 M SODIUM ACETATE AND 15% (W/V) PEG 4K, WITH A PROTEIN CONCENTRATION OF 20 MG ML-1. CRYSTALS WERE SOAKED WITH 10 MM NADPH FOR 5 MIN

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorDate: Dec 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→139 Å / Num. obs: 133601 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P19
Resolution: 2.5→139.04 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.888 / SU B: 9.134 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25055 6490 5.1 %RANDOM
Rwork0.23388 ---
obs0.23472 121980 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.145 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å20 Å20.48 Å2
2---2.07 Å20 Å2
3---3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.5→139.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18922 0 480 290 19692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01919709
X-RAY DIFFRACTIONr_bond_other_d0.0080.0219175
X-RAY DIFFRACTIONr_angle_refined_deg1.6042.00126878
X-RAY DIFFRACTIONr_angle_other_deg1.16343616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02552549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53422.623793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.971153028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.59415215
X-RAY DIFFRACTIONr_chiral_restr0.0840.23206
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222430
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024489
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_it2.4733.50410236
X-RAY DIFFRACTIONr_mcbond_other2.4733.50410235
X-RAY DIFFRACTIONr_mcangle_it3.7285.24612771
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.73.6399473
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A155170.02
12B155170.02
21A154460.03
22C154460.03
31A154620.03
32D154620.03
41A155010.03
42E155010.03
51A153380.03
52F153380.03
61A152240.02
62G152240.02
71A151950.02
72H151950.02
81A143200.03
82I143200.03
91A147520.03
92J147520.03
101B154820.04
102C154820.04
111B155470.04
112D155470.04
121B155830.04
122E155830.04
131B153600.04
132F153600.04
141B152520.03
142G152520.03
151B152280.03
152H152280.03
161B142150.04
162I142150.04
171B148640.03
172J148640.03
181C155190.02
182D155190.02
191C155790.03
192E155790.03
201C153930.03
202F153930.03
211C152880.03
212G152880.03
221C152620.03
222H152620.03
231C142320.04
232I142320.04
241C147850.03
242J147850.03
251D156020.03
252E156020.03
261D154670.03
262F154670.03
271D152690.02
272G152690.02
281D152440.02
282H152440.02
291D142510.03
292I142510.03
301D148190.03
302J148190.03
311E154300.04
312F154300.04
321E153080.03
322G153080.03
331E152810.03
332H152810.03
341E142570.04
342I142570.04
351E148270.03
352J148270.03
361F152130.04
362G152130.04
371F151860.04
372H151860.04
381F142620.04
382I142620.04
391F147700.03
392J147700.03
401G152910.03
402H152910.03
411G142610.03
412I142610.03
421G146450.03
422J146450.03
431H141690.04
432I141690.04
441H146410.03
442J146410.03
451I142610.03
452J142610.03
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 494 -
Rwork0.286 8963 -
obs--99.74 %

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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

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