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- PDB-3r8r: Transaldolase from Bacillus subtilis -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3r8r
TitleTransaldolase from Bacillus subtilis
ComponentsTransaldolase
KeywordsTRANSFERASE / transaldolase / pentose phosphate pathway / Schiff Bases
Function / homology
Function and homology information


transaldolase / transaldolase activity / aldehyde-lyase activity / pentose-phosphate shunt / carbohydrate metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Transaldolase type 3B, putative / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel ...Transaldolase type 3B, putative / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchneider, G. / Sandalova, T. / Samland, A.
CitationJournal: Febs J. / Year: 2012
Title: Conservation of structure and mechanism within the transaldolase enzyme family.
Authors: Samland, A.K. / Baier, S. / Schurmann, M. / Inoue, T. / Huf, S. / Schneider, G. / Sprenger, G.A. / Sandalova, T.
History
DepositionMar 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 29, 2020Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.4Sep 13, 2023Group: 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 / 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 / _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: Transaldolase
B: Transaldolase
C: Transaldolase
D: Transaldolase
E: Transaldolase
F: Transaldolase
G: Transaldolase
H: Transaldolase
I: Transaldolase
J: Transaldolase
V: Transaldolase
K: Transaldolase
L: Transaldolase
M: Transaldolase
N: Transaldolase
W: Transaldolase
P: Transaldolase
R: Transaldolase
T: Transaldolase
U: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,85150
Polymers460,00920
Non-polymers2,84230
Water61,1973397
1
A: Transaldolase
B: Transaldolase
C: Transaldolase
D: Transaldolase
E: Transaldolase
F: Transaldolase
G: Transaldolase
H: Transaldolase
I: Transaldolase
J: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,42625
Polymers230,00510
Non-polymers1,42115
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41580 Å2
ΔGint-413 kcal/mol
Surface area70890 Å2
MethodPISA
2
V: Transaldolase
K: Transaldolase
L: Transaldolase
M: Transaldolase
N: Transaldolase
W: Transaldolase
P: Transaldolase
R: Transaldolase
T: Transaldolase
U: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,42625
Polymers230,00510
Non-polymers1,42115
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41140 Å2
ΔGint-409 kcal/mol
Surface area71270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.299, 127.280, 158.448
Angle α, β, γ (deg.)90.00, 98.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31U
41T
51E
61F
71G
81H
91I
101R
111K
121L
131M
141W
151V
12C
22D
32J
42N
52P

NCS domain segments:

Component-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMET5AA1 - 2121 - 212
21METMET5BB1 - 2121 - 212
31METMET5UT1 - 2121 - 212
41METMET5TS1 - 2121 - 212
51METMET5EE1 - 2121 - 212
61METMET5FF1 - 2121 - 212
71METMET5GG1 - 2121 - 212
81METMET5HH1 - 2121 - 212
91METMET5II1 - 2121 - 212
101METMET5RR1 - 2121 - 212
111METMET5KL1 - 2121 - 212
121METMET5LM1 - 2121 - 212
131METMET5MN1 - 2121 - 212
141METMET5WP1 - 2121 - 212
151METMET5VK1 - 2121 - 212
12HISHIS2CC41 - 21241 - 212
22HISHIS2DD41 - 21241 - 212
32HISHIS2JJ41 - 21241 - 212
42HISHIS2NO41 - 21241 - 212
52HISHIS2PQ41 - 21241 - 212

NCS ensembles :
ID
1
2

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Components

#1: Protein
Transaldolase / / 20 kDa phosphoprotein orfU / CSI9


Mass: 23000.453 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU37110, tal, ywjH / Production host: Escherichia coli (E. coli) / References: UniProt: P19669, transaldolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3397 / 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: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 293 K / pH: 9
Details: 20% PEG 4K, 0.2M of Li2SO4, 20% of glycerol, 100 mM Tris/HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.092
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2004
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.092 Å / Relative weight: 1
ReflectionResolution: 1.9→69 Å / Num. obs: 441576 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L6W
Resolution: 1.9→58.93 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.34 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 22163 5 %RANDOM
Rwork0.2 ---
obs0.202 419370 100 %-
all-419370 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.07 Å2
2--0.13 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→58.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31905 0 160 3397 35462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02232504
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221248
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.96944071
X-RAY DIFFRACTIONr_angle_other_deg0.887352428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42954167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4325.031326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.589155728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.82515160
X-RAY DIFFRACTIONr_chiral_restr0.0690.25366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0235709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025863
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_it0.5041.520790
X-RAY DIFFRACTIONr_mcbond_other0.1341.58513
X-RAY DIFFRACTIONr_mcangle_it0.954233540
X-RAY DIFFRACTIONr_scbond_it1.458311714
X-RAY DIFFRACTIONr_scangle_it2.4944.510531
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
21C1014tight positional0.030.05
22D1014tight positional0.020.05
23J1014tight positional0.020.05
24N1014tight positional0.020.05
25P1014tight positional0.030.05
11A1238medium positional0.080.5
12B1238medium positional0.130.5
13U1238medium positional0.090.5
14T1238medium positional0.130.5
15E1238medium positional0.090.5
16F1238medium positional0.10.5
17G1238medium positional0.090.5
18H1238medium positional0.180.5
19I1238medium positional0.110.5
110R1238medium positional0.140.5
111K1238medium positional0.090.5
112L1238medium positional0.140.5
113M1238medium positional0.120.5
114W1238medium positional0.10.5
115V1238medium positional0.110.5
21C1174medium positional0.020.5
22D1174medium positional0.020.5
23J1174medium positional0.020.5
24N1174medium positional0.020.5
25P1174medium positional0.020.5
11A1423loose positional0.165
12B1423loose positional0.195
13U1423loose positional0.175
14T1423loose positional0.25
15E1423loose positional0.155
16F1423loose positional0.175
17G1423loose positional0.165
18H1423loose positional0.255
19I1423loose positional0.185
110R1423loose positional0.25
111K1423loose positional0.175
112L1423loose positional0.215
113M1423loose positional0.185
114W1423loose positional0.185
115V1423loose positional0.175
21C1014tight thermal0.320.5
22D1014tight thermal0.120.5
23J1014tight thermal0.10.5
24N1014tight thermal0.090.5
25P1014tight thermal0.110.5
11A1238medium thermal0.372
12B1238medium thermal0.32
13U1238medium thermal0.462
14T1238medium thermal0.392
15E1238medium thermal0.442
16F1238medium thermal0.312
17G1238medium thermal0.482
18H1238medium thermal0.482
19I1238medium thermal0.312
110R1238medium thermal0.312
111K1238medium thermal0.352
112L1238medium thermal0.342
113M1238medium thermal0.52
114W1238medium thermal0.342
115V1238medium thermal0.42
21C1174medium thermal0.222
22D1174medium thermal0.082
23J1174medium thermal0.092
24N1174medium thermal0.072
25P1174medium thermal0.092
11A1423loose thermal0.3910
12B1423loose thermal0.3710
13U1423loose thermal0.4510
14T1423loose thermal0.4110
15E1423loose thermal0.4410
16F1423loose thermal0.3510
17G1423loose thermal0.4410
18H1423loose thermal0.4910
19I1423loose thermal0.3510
110R1423loose thermal0.3710
111K1423loose thermal0.3510
112L1423loose thermal0.3410
113M1423loose thermal0.4510
114W1423loose thermal0.410
115V1423loose thermal0.4210
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 1670 -
Rwork0.311 30813 -
obs--99.99 %
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)
10.1318-0.10890.11470.7714-0.49791.06220.0230.0359-0.0981-0.06470.0317-0.07170.15220.0855-0.05480.04250.0364-0.00790.0488-0.03980.115355.255-25.725-8.443
20.2749-0.1020.19550.730.10.2609-0.0219-0.0849-0.06760.27740.0546-0.01830.0073-0.0655-0.03260.18960.0366-0.04150.07050.03160.042249.528-17.77724.889
30.20720.1656-0.14381.939-0.41640.245-0.0296-0.07580.01730.49030.0062-0.1432-0.06010.00370.02340.19960.0285-0.07330.0811-0.02230.031547.90816.5727.605
40.63130.0964-0.34260.2757-0.11660.8202-0.03820.02510.15570.03310.0338-0.0286-0.1237-0.00730.00430.0496-0.02-0.0350.03830.00590.065552.82729.864-3.461
50.42220.01690.00751.25170.16970.3908-0.04450.0731-0.0395-0.17130.0723-0.1296-0.02920.0844-0.02780.0612-0.0430.04640.1055-0.02590.036657.4434.074-26.133
60.574-0.10390.20710.6742-0.18170.61440.05380.0651-0.1617-0.0813-0.00230.17170.01560.0469-0.05140.0503-0.012-0.05050.0421-0.03230.114123.256-20.751-23.301
70.2725-0.1640.15811.50890.41250.3398-0.04720.05510.0306-0.2791-0.00430.1459-0.094-0.00180.05140.129-0.0193-0.06940.07050.01480.037623.19813.475-29.002
80.4632-0.0463-0.39190.38610.13940.65990.0042-0.0630.14830.01030.01040.146-0.06290.0424-0.01470.03210.0286-0.00920.0463-0.02250.130817.16529.1571.435
90.573-0.0956-0.0841.2213-0.01860.3195-0.0862-0.1846-0.0730.31860.02010.27840.0391-0.08980.0660.15560.02770.13620.15860.01360.12314.165.11925.934
100.32580.06420.23731.05770.93471.37640.0093-0.1109-0.19650.3848-0.00730.28070.2949-0.1313-0.0020.1741-0.02710.11870.08580.09370.254917.4-25.83210.625
110.57430.0557-0.06990.90220.01570.3902-0.0360.0877-0.0309-0.10330.0278-0.09970.00260.08610.00830.0506-0.02670.04320.1251-0.01380.037846.352-61.06752.519
120.1264-0.01830.17650.6038-0.64741.01470.03570.0562-0.1198-0.1409-0.0021-0.08520.17850.118-0.03360.08180.0592-0.00060.1014-0.02990.141443.235-91.44569.388
130.67810.01040.06940.77850.22510.46090.0702-0.1072-0.10590.1596-0.027-0.0837-0.0229-0.0531-0.04330.11210.0074-0.04230.07140.0550.064437.423-84.562102.924
140.31360.31090.04781.5957-0.40240.2176-0.0383-0.12670.00550.3231-0.0231-0.1282-0.0832-0.03930.06150.17560.0351-0.04280.1232-0.02050.052237.294-50.049106.552
150.82560.1697-0.49640.1214-0.18720.90560.01180.06450.18250.02870.01520.0127-0.1427-0.0249-0.0270.0507-0.0343-0.01740.06480.01910.085842.837-35.71575.627
160.1892-0.14170.11461.49060.44660.3495-0.0490.04760.0395-0.2433-0.00030.1136-0.09320.00180.04920.1135-0.021-0.06340.07320.02770.040912.449-50.59849.848
170.4923-0.2289-0.60250.14790.30021.07610.0396-0.07780.1386-0.03280.0259-0.0024-0.15340.0423-0.06550.05760.019-0.02180.0786-0.02620.15956.948-35.34680.689
180.5220.00180.05011.65690.07240.3579-0.0351-0.1276-0.02520.22360.01050.18860.0061-0.08570.02450.10820.03340.10540.14730.0270.10472.911-60.148104.553
190.11720.14780.27650.77790.73231.13240.0549-0.0806-0.08130.2273-0.02160.16930.1861-0.1035-0.03340.0902-0.03360.04560.09870.07520.19125.32-90.7588.096
200.34880.00320.19670.6385-0.22360.59660.02840.0474-0.0691-0.07560.04820.09170.01090.0466-0.07650.0571-0.022-0.05180.047-0.01030.073711.318-84.93854.371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 212
2X-RAY DIFFRACTION2B1 - 212
3X-RAY DIFFRACTION3C1 - 220
4X-RAY DIFFRACTION4D1 - 212
5X-RAY DIFFRACTION5E1 - 212
6X-RAY DIFFRACTION6F1 - 212
7X-RAY DIFFRACTION7G1 - 212
8X-RAY DIFFRACTION8H1 - 212
9X-RAY DIFFRACTION9I1 - 212
10X-RAY DIFFRACTION10J1 - 212
11X-RAY DIFFRACTION11V1 - 212
12X-RAY DIFFRACTION12K1 - 212
13X-RAY DIFFRACTION13L1 - 212
14X-RAY DIFFRACTION14M1 - 212
15X-RAY DIFFRACTION15N1 - 212
16X-RAY DIFFRACTION16W1 - 212
17X-RAY DIFFRACTION17P1 - 212
18X-RAY DIFFRACTION18R1 - 212
19X-RAY DIFFRACTION19T1 - 212
20X-RAY DIFFRACTION20U1 - 212

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Yorodumi

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  • 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

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