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- PDB-4odi: 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutas... -

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Basic information

Entry
Database: PDB / ID: 4odi
Title2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 from Toxoplasma gondii
ComponentsPhosphoglycerate mutase PGMII
KeywordsISOMERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Phosphoglycerate mutase-like
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / : / glycolytic process
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglycerate mutase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMinasov, G. / Ruan, J. / Ngo, H. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Shanmugam, D. / Roos, D. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Front Cell Infect Microbiol / Year: 2018
Title: CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii .
Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. ...Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. / Moulton, J.D. / Moulton, H. / McPhillie, M.J. / Muench, S.P. / Fishwick, C.W.G. / Sabini, E. / Shanmugam, D. / Roos, D.S. / McLeod, R. / Anderson, W.F. / Ngo, H.M.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 27, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_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_label_asym_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_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.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
Revision 1.3Sep 20, 2023Group: Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate mutase PGMII
B: Phosphoglycerate mutase PGMII
C: Phosphoglycerate mutase PGMII
D: Phosphoglycerate mutase PGMII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0388
Polymers127,9464
Non-polymers924
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-90 kcal/mol
Surface area41210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.182, 149.474, 72.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA15 - 25615 - 256
21GLUGLUBB15 - 25615 - 256
12GLUGLUAA15 - 25615 - 256
22GLUGLUCC15 - 25615 - 256
13ASPASPAA17 - 24717 - 247
23ASPASPDD17 - 24717 - 247
14GLUGLUBB15 - 25615 - 256
24GLUGLUCC15 - 25615 - 256
15ASPASPBB17 - 24717 - 247
25ASPASPDD17 - 24717 - 247
16ASPASPCC17 - 24717 - 247
26ASPASPDD17 - 24717 - 247

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Phosphoglycerate mutase PGMII


Mass: 31986.537 Da / Num. of mol.: 4 / Fragment: UNP residues 75-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: PGMII, TGME49_297060 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: S8GJT7, bisphosphoglycerate mutase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein - 7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, Screen - Classics II (G12), 0.2M Magnesium chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, ...Details: Protein - 7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, Screen - Classics II (G12), 0.2M Magnesium chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2013 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 33033 / Num. obs: 33033 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 18.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1604 / Rsym value: 0.645 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XQ9
Resolution: 2.6→29.72 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 21.851 / SU ML: 0.232
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23881 1671 5.1 %RANDOM
Rwork0.19717 ---
all0.19925 31317 --
obs0.19925 31317 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.296 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20 Å2
2--2.24 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7719 0 4 164 7887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197937
X-RAY DIFFRACTIONr_bond_other_d0.0060.027631
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.96210788
X-RAY DIFFRACTIONr_angle_other_deg1.217317624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3825966
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11224.101356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.868151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5541549
X-RAY DIFFRACTIONr_chiral_restr0.0920.21183
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218821
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021732
X-RAY DIFFRACTIONr_mcbond_it2.2682.4863870
X-RAY DIFFRACTIONr_mcbond_other2.2552.4853869
X-RAY DIFFRACTIONr_mcangle_it3.5413.7254834
X-RAY DIFFRACTIONr_mcangle_other3.5423.7264835
X-RAY DIFFRACTIONr_scbond_it3.0032.7784067
X-RAY DIFFRACTIONr_scbond_other3.0032.7764065
X-RAY DIFFRACTIONr_scangle_other4.754.0215954
X-RAY DIFFRACTIONr_long_range_B_refined6.81520.259103
X-RAY DIFFRACTIONr_long_range_B_other6.81520.2119080
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A146320.13
12B146320.13
21A143910.14
22C143910.14
31A137520.13
32D137520.13
41B143610.13
42C143610.13
51B137660.12
52D137660.12
61C137820.12
62D137820.12
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 94 -
Rwork0.259 2253 -
obs--98.24 %
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)
12.590.487-0.49531.5547-0.38210.23650.1379-0.08870.23920.2607-0.08930.0137-0.01370.094-0.04870.1009-0.005-0.02490.1965-0.03790.146336.746327.48135.4492
210.42935.5866-9.09117.1207-3.158.6426-0.3473-0.5687-0.11930.1574-0.08570.64760.47890.570.4330.2101-0.00350.01710.26320.02570.277221.066414.577.8608
317.2411-11.7723-15.114426.439611.479421.53690.5447-0.88530.05681.5713-0.8772-0.23731.2471-0.37950.33250.6506-0.26950.08140.4307-0.02820.396420.34435.457616.03
43.0823-0.2076-0.81141.4706-0.5381.6158-0.02470.0173-0.36590.11420.02440.20670.0537-0.09270.00030.0403-0.0368-0.01230.0968-0.03040.203323.558415.526-2.1968
52.64730.0046-0.82471.9884-0.23741.2709-0.0632-0.2724-0.15980.27550.1284-0.11290.10160.0651-0.06520.05990.0256-0.05470.187-0.02760.153543.323217.34690.8005
631.2095-1.19698.58141.273-3.21739.7116-0.7336-1.6108-1.5367-0.0098-0.1118-0.4620.19170.58710.84540.55120.14790.06710.72180.13150.375445.08917.04318.296
71.84011.1907-0.21592.4993-0.17641.10890.1866-0.2056-0.09270.3526-0.22020.0758-0.071-0.00440.03360.0757-0.0088-0.00390.1272-0.04040.102427.434246.97332.7135
87.93356.43391.850411.08934.64553.83170.17230.07510.29110.2772-0.229-0.3354-0.06830.24150.05670.0368-0.0311-0.04410.15260.05110.160739.794354.6505-5.2798
97.0153-5.456.528512.97162.463723.0624-0.3605-0.02160.68020.5665-0.36870.3254-1.27020.73680.72920.3778-0.12360.03220.4314-0.07590.430144.454471.45111.1361
104.12860.35020.77571.98160.11311.5228-0.05530.08950.3107-0.0431-0.0111-0.1595-0.18840.10680.06640.03720.0009-0.00620.1106-0.02230.113236.160753.442-10.0909
112.03670.15360.21063.37961.01574.5076-0.04330.01330.2874-0.05370.02970.2909-0.269-0.21550.01350.03340.04270.01590.1439-0.05320.213218.833757.0156-6.757
1226.1805-5.7046-4.840313.4166-0.00754.3169-1.0716-1.14031.6693-0.08661.05350.6907-0.4992-0.14730.01810.2849-0.0305-0.08140.3361-0.23950.453119.433561.92568.4957
134.8369-0.9839-0.72185.19330.57145.0711-0.15520.3976-0.0182-1.7468-0.01010.80570.39880.02770.16530.7021-0.0346-0.25770.0380.00120.168326.733114.0261-33.4001
142.9929-0.5910.85743.6131-0.61912.6875-0.20320.23710.171-1.19220.16480.4280.18070.03470.03840.5017-0.0783-0.22040.14130.03430.116826.166121.7083-33.6074
153.39020.1934-3.544313.61724.734311.82820.18520.5408-0.7498-1.04490.08070.01491.27160.0891-0.26590.96520.1871-0.23820.3756-0.13970.431336.6884-5.2475-34.1124
163.0116-0.3792-0.64673.9537-0.20291.7177-0.06160.0131-0.2041-0.66550.13290.32010.35660.0876-0.07130.22930.021-0.11980.0681-0.04780.111230.389111.6292-21.8954
174.94492.98272.40724.96580.38766.7297-0.09420.04890.1185-0.9425-0.20141.61540.5284-0.61930.29560.3931-0.0538-0.48890.265-0.05511.038113.641813.539-26.9161
1821.8627-13.5707-0.454917.94749.18298.3592-0.2668-0.0657-1.74130.4460.25480.93470.281-0.02770.0120.923-0.2816-0.22210.9317-0.08660.550913.26319.4517-41.2149
194.2922-0.84740.78654.0095-0.27684.6755-0.25190.55190.0291-1.92480.1272-0.4811-0.02760.35750.12471.133-0.28430.24960.2556-0.02950.062237.880739.4074-42.1474
202.5566-0.59161.12625.29060.64530.727-0.20.2829-0.1972-1.42670.2801-0.1536-0.24530.1917-0.08010.7377-0.10660.06390.1943-0.01370.074234.065138.5906-34.4846
215.4409-0.5692-0.40266.81211.24816.46220.18310.94420.4055-0.2653-0.1341-0.4326-1.58070.08-0.0491.37150.0077-0.32080.23890.18150.34627.254260.9013-41.5514
223.62650.56841.58873.6521.11662.4333-0.37860.12880.1886-1.28090.36-0.247-0.68190.17760.01860.544-0.10240.06250.13090.03580.087733.696446.516-27.8788
237.44030.48816.44668.7306-1.22477.0853-1.04821.295-0.0259-2.53491.1665-1.6596-1.28381.597-0.11831.4671-0.88620.8530.9093-0.26620.668147.449649.5637-34.4399
244.7143-2.81989.02277.21934.623235.4170.17440.25140.3872-0.67340.5601-1.0639-0.71641.7631-0.73450.3131-0.24950.29620.4919-0.00420.51953.423242.3337-33.9318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 102
2X-RAY DIFFRACTION2A103 - 114
3X-RAY DIFFRACTION3A115 - 129
4X-RAY DIFFRACTION4A130 - 187
5X-RAY DIFFRACTION5A188 - 247
6X-RAY DIFFRACTION6A248 - 257
7X-RAY DIFFRACTION7B15 - 96
8X-RAY DIFFRACTION8B97 - 114
9X-RAY DIFFRACTION9B115 - 129
10X-RAY DIFFRACTION10B130 - 208
11X-RAY DIFFRACTION11B209 - 246
12X-RAY DIFFRACTION12B247 - 259
13X-RAY DIFFRACTION13C15 - 45
14X-RAY DIFFRACTION14C46 - 110
15X-RAY DIFFRACTION15C111 - 129
16X-RAY DIFFRACTION16C130 - 217
17X-RAY DIFFRACTION17C218 - 244
18X-RAY DIFFRACTION18C245 - 257
19X-RAY DIFFRACTION19D17 - 64
20X-RAY DIFFRACTION20D65 - 114
21X-RAY DIFFRACTION21D115 - 146
22X-RAY DIFFRACTION22D147 - 208
23X-RAY DIFFRACTION23D209 - 234
24X-RAY DIFFRACTION24D235 - 248

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