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- PDB-4pv2: Crystal structure of potassium-dependent plant-type L-asparaginas... -

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Basic information

Entry
Database: PDB / ID: 4pv2
TitleCrystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with K+ and Na+ cations
Components(L-ASPARAGINASE ...Asparaginase) x 2
KeywordsHYDROLASE / metal binding sites / potassium coordination / K-dependent enzyme / Ntn-hydrolase / plant protein / L-asparaginase / isoaspartyl aminopeptidase / amidohydrolase
Function / homology
Function and homology information


(Glycosyl)asparaginase / Peptidase T2, asparaginase 2 / Asparaginase / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NITRATE ION / Isoaspartyl peptidase/L-asparaginase 2
Similarity search - Component
Biological speciesPhaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBejger, M. / Gilski, M. / Imiolczyk, B. / Clavel, D. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Na+/K+ exchange switches the catalytic apparatus of potassium-dependent plant L-asparaginase
Authors: Bejger, M. / Imiolczyk, B. / Clavel, D. / Gilski, M. / Pajak, A. / Marsolais, F. / Jaskolski, M.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of plant asparaginase
Authors: Michalska, K. / Bujacz, G. / Jaskolski, M.
#2: Journal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate
Authors: Michalska, K. / Brzezinski, K. / Jaskolski, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Crystal packing of plant-type L-asparaginase from Escherichia coli
Authors: Michalska, K. / Borek, D. / Hernandez-Santoyo, A. / Jaskolski, M.
#4: Journal: J.Biol.Chem. / Year: 2008
Title: The mechanism of autocatalytic activation of plant-type L-asparaginases
Authors: Michalska, K. / Hernandez-Santoyo, A. / Jaskolski, M.
#5: Journal: ACTA BIOCHIM.POL. / Year: 2006
Title: Structural aspects of L-asparaginases, their friends and relations
Authors: Michalska, K. / Jaskolski, M.
#6: Journal: Eur.J.Biochem. / Year: 2004
Title: Expression, purification and catalytic activity of Lupinus luteus asparagine -amidohydrolase and its Escherichia coli homolog
Authors: Borek, D. / Michalska, K. / Brzezinski, K. / Kisiel, A. / Podkowi ski, J. / Bonthron, D.T. / Krowarsch, D. / Otlewski, J. / Jaskolski, M.
#7: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by Escherichia coli genome
Authors: Borek, D. / Jaskolski, M.
#8: Journal: ACTA BIOCHIM.POL. / Year: 2001
Title: Sequence analysis of enzymes with asparaginase activity
Authors: Borek, D. / Jaskolski, M.
#9: Journal: Biochemistry / Year: 2012
Title: Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis
Authors: Nomme, J. / Su, Y. / Konrad, M. / Lavie, A.
#10: Journal: Chem.Biol. / Year: 2013
Title: Free glicyne accelerates the autoproteolytic activation of human asparaginase
Authors: Su, Y. / Karamitros, C.S. / Nomme, J. / McSorley, T. / Konrad, M. / Lavie, A.
History
DepositionMar 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: L-ASPARAGINASE ALPHA SUBUNIT
B: L-ASPARAGINASE BETA SUBUNIT
C: L-ASPARAGINASE ALPHA SUBUNIT
D: L-ASPARAGINASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,83133
Polymers69,2814
Non-polymers1,55029
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-93 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.885, 102.632, 123.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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L-ASPARAGINASE ... , 2 types, 4 molecules ACBD

#1: Protein L-ASPARAGINASE ALPHA SUBUNIT / L-ASPARAGINE AMIDOHYDROLASE


Mass: 21015.805 Da / Num. of mol.: 2 / Fragment: N-TERMINAL SUBUNIT ALPHA (UNP residues 1-195)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: PHAVU_001G025000g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V7CU13, asparaginase
#2: Protein L-ASPARAGINASE BETA SUBUNIT / L-ASPARAGINE AMIDOHYDROLASE


Mass: 13624.618 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SUBUNIT BETA (UNP residues 196-326)
Source method: isolated from a genetically manipulated source
Details: SUBUNITS ALPHA (CHAINS A, C) AND BETA (CHAINS B, D) ARE, RESPECTIVELY, THE N- AND C-TERMINAL PRODUCTS OF AUTOPROTEOLYTIC CLEAVAGE OF A PRECURSOR.
Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: PHAVU_001G025000g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V7CU13, asparaginase

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Non-polymers , 4 types, 450 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical...
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE DIFFERENCE (POLYMORPHISM) AT POSITION 17 REFLECTS A DIFFERENT CULTIVAR (AC COMPASS).

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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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG3350, 0.1M bis tris propane, 0.2M sodium nitrate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.827 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 9, 2012
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.79→38.77 Å / Num. all: 68445 / Num. obs: 68445 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.33
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.98 / Num. unique all: 10836 / % possible all: 98.2

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PU6

4pu6


Resolution: 1.79→38.77 Å / SU ML: 0.19 / Isotropic thermal model: Isotropic / Cross valid method: R free / Phase error: 20.4 / Stereochemistry target values: Engh & Huber / Details: H ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 1232 1.8 %RANDOM
Rwork0.1635 ---
all0.1643 68445 --
obs0.1643 68445 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 92 421 4741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194453
X-RAY DIFFRACTIONf_angle_d1.3735992
X-RAY DIFFRACTIONf_dihedral_angle_d14.3021593
X-RAY DIFFRACTIONf_chiral_restr0.097687
X-RAY DIFFRACTIONf_plane_restr0.006791
LS refinement shellResolution: 1.79→1.86 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2708 132 -
Rwork0.2431 7232 -
obs-7232 98 %
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)
13.179-1.4561-2.16485.81366.78798.06840.23490.1765-0.4579-0.7136-0.2803-0.5965-0.1050.2626-0.34130.37890.12720.15560.20690.07170.390218.7659-11.51320.8294
21.9932-2.2232.20965.0022-4.91054.8252-0.7611-0.42440.96421.5417-0.3434-1.8338-1.38381.06970.98980.4604-0.0052-0.25070.78630.08540.692126.5576-4.413640.7672
36.18080.13683.08395.26491.46797.1581-0.0738-0.5143-0.59760.0295-0.0621-0.50250.60750.4534-0.01860.22670.08810.13030.27170.17060.449519.0369-16.77831.4906
42.1992-0.14720.64432.5906-0.2184.0922-0.0802-0.0474-0.3547-0.0853-0.10130.04660.21580.1620.08380.18590.01680.05240.1240.04340.28349.2059-11.231528.2471
56.6653-0.61471.20624.3099-5.53037.1287-0.1424-0.72170.77440.6393-0.0544-0.0027-0.5811-0.29730.20130.3092-0.00580.02230.2174-0.04760.265.56683.396642.1994
63.49510.0159-2.47323.6954-1.715.8722-0.07340.1851-0.1118-0.2534-0.00120.17860.5435-0.22240.08380.1428-0.0401-0.00530.1052-0.0150.16734.085-1.400423.0717
75.6289-1.67640.55962.1448-1.1814.48420.04810.447-0.3663-0.2424-0.08130.1370.2011-0.4093-0.07550.1552-0.02540.00460.174-0.01020.224-1.3471-1.786221.0248
86.43984.4498-0.11715.7395-1.27774.16260.0123-0.05860.02560.23040.15810.70310.1026-0.4311-0.13190.1276-0.00210.04340.15410.03190.2902-5.77711.37728.9025
97.63881.60024.12013.54731.22657.13470.3737-1.03930.04240.9954-0.4217-0.02260.5695-0.04850.03240.4257-0.0240.03470.30910.04850.19436.5432-3.018344.4278
101.7195-0.5601-0.2263.395-0.39321.971-0.04330.1189-0.0967-0.1513-0.1327-0.16630.2220.17220.1160.1187-0.01180.03090.16090.03740.191212.4238-0.103524.2653
116.9043-3.78462.86768.1434-4.87143.8088-0.0108-0.06330.15021.1084-0.1764-1.9223-0.78711.1430.11340.2768-0.0748-0.07480.29250.07230.570118.494310.804126.2371
126.4283-3.9525-1.42673.47181.8221.1847-0.12180.4125-0.2017-0.8413-0.6328-0.78640.30650.9450.18050.3420.07140.18110.41560.13940.397322.15454.564211.4718
132.82271.0892-0.44664.881-1.09275.9253-0.15170.05810.02190.0284-0.5136-1.1273-0.35581.498-0.15490.14990.00950.11110.64620.30710.70628.68623.385717.5514
146.5792-1.98170.15744.85464.70055.5007-0.4263-0.36570.6649-0.9590.1766-0.9247-0.99290.8308-0.05810.3372-0.05760.02630.3320.1120.460823.84463.475824.1756
152.6761-0.45092.15332.51531.64455.6694-0.32230.1284-0.2377-0.2053-0.4285-0.62330.821.5450.14730.37620.08280.24360.44640.14210.489124.2469-6.769917.0549
166.1627-0.84080.22662.5496-2.73593.7847-0.14150.2019-0.0565-0.0825-0.4664-0.81350.29050.87410.22650.26280.06580.120.36620.19040.466425.0732-9.688424.6511
171.49162.28981.63887.66884.95627.6372-0.05160.1555-0.0862-0.5033-0.0042-1.47940.11291.744-0.25160.19730.16280.06650.62720.21610.671428.426-10.914629.7647
182.5193-2.05182.61622.7237-1.08063.74820.20170.0822-0.4088-0.49780.03070.05940.0034-0.2026-0.21260.2481-0.00880.01660.1616-0.03490.08840.748627.77249.1185
195.35182.37326.47852.90612.24478.0393-0.135-0.00640.5643-0.0651-0.07750.0947-0.6491-0.33330.2750.31830.02550.02090.15930.00190.137-1.419136.002912.8
203.2876-0.48120.30751.802-0.1013.17670.0417-0.16870.08060.1574-0.04350.2352-0.2433-0.23930.00710.1876-0.00760.02560.1345-0.02580.1013-1.720526.756223.405
213.5002-0.5996-0.91763.082-0.26643.2218-0.0293-0.41410.00580.54470.0085-0.0082-0.19150.2154-0.00790.2281-0.0479-0.00390.1698-0.0110.08635.510220.677732.2096
225.12742.83533.67953.65481.38456.03740.0010.2275-0.0796-0.2803-0.41160.8273-0.0018-1.63330.2070.20070.01940.01620.7161-0.14770.5206-17.011218.658320.7828
232.86530.228-0.70622.3597-1.16672.4665-0.0019-0.11370.0728-0.0959-0.02480.0352-0.09590.12280.0270.139-0.02980.01470.1277-0.03620.07684.536222.44619.6712
240.03460.0109-0.29984.5156-0.99023.26060.06090.15970.0986-0.0385-0.02850.02590.06290.1353-0.04440.1078-0.01630.0080.1382-0.0090.07328.373416.482618.1973
257.4252-5.66130.35377.0328-1.76362.4545-0.34680.6439-0.9325-0.64110.30960.92750.5979-0.0937-0.02780.3196-0.07740.01520.2357-0.02830.2394.28428.758812.551
267.84823.9582-5.56826.9004-3.08725.392-0.11470.0549-0.3303-0.4587-0.1825-0.87410.280.64310.29580.21650.04350.07140.29450.04520.196419.25615.25749.2008
275.5063-1.2905-1.04741.5097-1.88194.55030.0650.7064-0.574-0.8085-0.16440.07230.4612-0.18530.01720.3143-0.00830.02490.2473-0.06710.176710.062616.30365.0161
284.8666-1.19610.11713.006-0.7892.55640.24820.40520.128-0.5921-0.1895-0.1409-0.23830.1847-0.05620.307-0.00460.05730.2340.01120.11278.284928.26266.7217
295.07262.81225.06853.53435.21718.387-0.05571.55460.1589-0.86010.2597-0.0364-0.26460.5542-0.16930.37220.0255-0.04010.34010.04790.19360.80330.60193.1034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 19 )
3X-RAY DIFFRACTION3chain 'A' and (resid 20 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 70 )
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 80 )
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 103 )
7X-RAY DIFFRACTION7chain 'A' and (resid 104 through 118 )
8X-RAY DIFFRACTION8chain 'A' and (resid 119 through 132 )
9X-RAY DIFFRACTION9chain 'A' and (resid 133 through 156 )
10X-RAY DIFFRACTION10chain 'B' and (resid 196 through 247 )
11X-RAY DIFFRACTION11chain 'B' and (resid 248 through 256 )
12X-RAY DIFFRACTION12chain 'B' and (resid 257 through 271 )
13X-RAY DIFFRACTION13chain 'B' and (resid 272 through 283 )
14X-RAY DIFFRACTION14chain 'B' and (resid 284 through 295 )
15X-RAY DIFFRACTION15chain 'B' and (resid 296 through 304 )
16X-RAY DIFFRACTION16chain 'B' and (resid 305 through 319 )
17X-RAY DIFFRACTION17chain 'B' and (resid 320 through 326 )
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 19 )
19X-RAY DIFFRACTION19chain 'C' and (resid 20 through 42 )
20X-RAY DIFFRACTION20chain 'C' and (resid 43 through 80 )
21X-RAY DIFFRACTION21chain 'C' and (resid 81 through 138 )
22X-RAY DIFFRACTION22chain 'C' and (resid 139 through 159 )
23X-RAY DIFFRACTION23chain 'D' and (resid 196 through 223 )
24X-RAY DIFFRACTION24chain 'D' and (resid 224 through 247 )
25X-RAY DIFFRACTION25chain 'D' and (resid 248 through 256 )
26X-RAY DIFFRACTION26chain 'D' and (resid 257 through 271 )
27X-RAY DIFFRACTION27chain 'D' and (resid 272 through 295 )
28X-RAY DIFFRACTION28chain 'D' and (resid 296 through 319 )
29X-RAY DIFFRACTION29chain 'D' and (resid 320 through 326 )

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  • 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

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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

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