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- PDB-2fty: Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri -

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Basic information

Entry
Database: PDB / ID: 2fty
TitleCrystal structure of dihydropyrimidinase from Saccharomyces kluyveri
Componentsdihydropyrimidinase
KeywordsHYDROLASE / alpha/beta barrel / beta-sandwich
Function / homology
Function and homology information


dihydropyrimidinase / dihydropyrimidinase activity / metal ion binding / cytoplasm
Similarity search - Function
Hydantoinase/dihydropyrimidinase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...Hydantoinase/dihydropyrimidinase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLachancea kluyveri (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDobritzsch, D. / Lohkamp, B.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: The Crystal Structures of Dihydropyrimidinases Reaffirm the Close Relationship between Cyclic Amidohydrolases and Explain Their Substrate Specificity.
Authors: Lohkamp, B. / Andersen, B. / Piskur, J. / Dobritzsch, D.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2005
Title: Crystallization and X-ray diffraction analysis of dihydropyrimidinase from Saccharomyces kluyveri
Authors: Dobritzsch, D. / Andersen, B. / Piskur, J.
History
DepositionJan 25, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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_conn_type / struct_ncs_dom_lim / 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_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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dihydropyrimidinase
B: dihydropyrimidinase
C: dihydropyrimidinase
D: dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,82412
Polymers249,3004
Non-polymers5238
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-403 kcal/mol
Surface area68770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.428, 73.320, 162.181
Angle α, β, γ (deg.)90.00, 91.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILESERSER2AA3 - 1032 - 102
21ILEILESERSER2BB3 - 1032 - 102
31ILEILESERSER2CC3 - 1032 - 102
41ILEILESERSER2DD3 - 1032 - 102
52GLYGLYGLUGLU2AA106 - 140105 - 139
62GLYGLYGLUGLU2BB106 - 140105 - 139
72GLYGLYGLUGLU2CC106 - 140105 - 139
82GLYGLYGLUGLU2DD106 - 140105 - 139
93VALVALARGARG2AA152 - 292151 - 291
103VALVALARGARG2BB152 - 292151 - 291
113VALVALARGARG2CC152 - 292151 - 291
123VALVALARGARG2DD152 - 292151 - 291
134ILEILEPROPRO2AA306 - 379305 - 378
144ILEILEPROPRO2BB306 - 379305 - 378
154ILEILEPROPRO2CC306 - 379305 - 378
164ILEILEPROPRO2DD306 - 379305 - 378
175ASNASNTYRTYR2AA382 - 540381 - 539
185ASNASNTYRTYR2BB382 - 540381 - 539
195ASNASNTYRTYR2CC382 - 540381 - 539
205ASNASNTYRTYR2DD382 - 540381 - 539
216ZNZNZNZN6AE - F601 - 602
226ZNZNZNZN6BG - H601 - 602
236ZNZNZNZN6CI - J601 - 602
246ZNZNZNZN6DK - L601 - 602
Detailsthe asymmetric unit contains the biological assembly, which is the homotetramer

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Components

#1: Protein
dihydropyrimidinase


Mass: 62325.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea kluyveri (fungus) / Gene: Pyd2 / Plasmid: P343 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9P903, dihydropyrimidinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.1M ammonium sulfate, 0.001mM zinc chloride, 0.1M bis-tris , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.4→44.3 Å / Num. all: 83629 / Num. obs: 83629 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 44.9 Å2 / Rsym value: 0.086 / Net I/σ(I): 13.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 12084 / Rsym value: 0.309 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1nfg
Resolution: 2.4→43.85 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.883 / SU B: 19.086 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.701 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 4233 5.1 %RANDOM
Rwork0.21712 ---
obs0.21996 79226 98.98 %-
all-79226 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.905 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.41 Å2
2--2.7 Å20 Å2
3----2.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16587 0 8 681 17276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02217032
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.96623090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87252131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51224.993729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.726152910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6791560
X-RAY DIFFRACTIONr_chiral_restr0.0810.22561
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212814
X-RAY DIFFRACTIONr_nbd_refined0.1910.27973
X-RAY DIFFRACTIONr_nbtor_refined0.30.211585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2998
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.212
X-RAY DIFFRACTIONr_mcbond_it0.2961.510920
X-RAY DIFFRACTIONr_mcangle_it0.493217185
X-RAY DIFFRACTIONr_scbond_it0.98337045
X-RAY DIFFRACTIONr_scangle_it1.5484.55898
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2036tight positional0.030.05
2B2036tight positional0.030.05
3C2036tight positional0.030.05
4D2036tight positional0.030.05
1A1927medium positional0.310.5
2B1927medium positional0.380.5
3C1927medium positional0.390.5
4D1927medium positional0.360.5
1A3loose positional0.415
2B3loose positional0.475
3C3loose positional0.175
4D3loose positional0.15
1A2036tight thermal0.050.5
2B2036tight thermal0.050.5
3C2036tight thermal0.060.5
4D2036tight thermal0.050.5
1A1927medium thermal0.382
2B1927medium thermal0.362
3C1927medium thermal0.392
4D1927medium thermal0.352
1A3loose thermal1.9410
2B3loose thermal0.7710
3C3loose thermal0.4610
4D3loose thermal1.0910
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 313 -
Rwork0.238 5758 -
obs--98.32 %
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)
11.7397-0.15110.17580.77650.01040.99330.0175-0.1872-0.08140.1092-0.04930.09240.1013-0.18730.0318-0.0879-0.03220.086-0.0896-0.0007-0.109548.314156.331477.8257
21.7118-0.44421.43453.6046-2.11275.2302-0.0473-0.00720.1787-0.04790.13740.3441-0.3783-0.4359-0.0901-0.1625-0.00670.09450.022-0.0642-0.010535.248764.707262.1814
30.67610.0444-0.01180.5950.60271.08280.01240.0427-0.03150.0096-0.0910.12720.1142-0.1850.0785-0.0755-0.00380.037-0.1212-0.0115-0.108642.714958.556550.7759
42.14793.0412-0.062510.3402-1.55151.96510.09610.0166-0.3612-0.2072-0.2912-0.13810.3371-0.02510.1951-0.07560.02410.0339-0.0939-0.0238-0.122656.13150.736953.892
50.95920.30.37690.701-0.04041.38540.04120.0093-0.2545-0.0889-0.01830.02740.2827-0.0675-0.023-0.0257-0.01010.0452-0.12750.011-0.050350.53945.377563.6135
60.69010.12580.28581.1969-0.3951.93620.064-0.1445-0.0910.15-0.1283-0.11290.1543-0.05930.0643-0.1168-0.03210.0559-0.07630.0249-0.076851.554652.29472.7439
71.81820.2559-0.16021.0958-0.0680.85810.06160.24760.1666-0.1167-0.05040.1035-0.1179-0.1259-0.0112-0.00320.0305-0.0349-0.09340.0116-0.150450.854764.30443.2569
81.48460.5136-2.16124.1832-2.19955.6259-0.1148-0.0213-0.1927-0.08880.19190.33540.304-0.4386-0.0771-0.1474-0.0072-0.05520.0279-0.05390.00836.214856.904916.8993
90.70020.00530.11850.2850.23391.0453-0.0054-0.04510.0194-0.0579-0.08610.1797-0.1511-0.19850.0916-0.07010.02120.0259-0.0988-0.0165-0.107843.289862.07930.0512
102.2582-2.30690.246710.4069-1.84451.73170.020.00270.30490.305-0.1992-0.0482-0.37950.02420.1791-0.0575-0.02150.0148-0.0556-0.0366-0.140356.926469.843127.571
111.2229-0.5445-0.37571.08960.17431.66210.03970.0830.278-0.0817-0.0373-0.0023-0.3932-0.0496-0.00250.05920.0067-0.0036-0.12320.0382-0.048452.831876.444313.0411
120.9571-0.84480.4872.9303-3.80927.1524-0.03380.0097-0.2772-0.2079-0.03920.10280.63470.07090.073-0.0027-0.02430.0267-0.122-0.0431-0.046148.968945.92522.2805
132.3179-0.3387-0.4031.16960.3551.05190.0328-0.30.2040.05440.0244-0.128-0.05270.2539-0.0572-0.0869-0.0308-0.0119-0.0579-0.0291-0.122883.65573.750776.6028
141.7057-0.8406-0.37534.51131.53382.425-0.1466-0.1847-0.4358-0.19790.282-0.24170.47580.408-0.1353-0.0845-0.0380.00720.0487-0.0040.042396.920459.329361.6688
150.8454-0.22630.13720.3994-0.16091.5592-0.01620.06260.0548-0.00990.0241-0.2346-0.16970.1737-0.0079-0.0898-0.0030.0321-0.08170.007-0.086290.203364.781351.1801
161.98172.9506-0.642412.0746-0.85582.89160.01890.1130.2962-0.3773-0.10680.1929-0.38360.03680.0879-0.12860.05970.0309-0.09150.0063-0.134976.49972.164751.9492
171.3837-0.0004-0.36270.80580.32381.57280.02820.16680.3168-0.1915-0.0318-0.0898-0.31170.15130.0036-0.0192-0.02790.0272-0.08790.0302-0.030281.780680.601559.8415
180.9736-0.1256-0.32521.74760.8782.16180.051-0.09560.17090.0563-0.040.0663-0.18390.1182-0.011-0.1661-0.02670.0148-0.0899-0.0091-0.081480.046176.293370.4838
192.52960.1720.57040.83470.17471.01110.06660.2758-0.172-0.08650.0133-0.08970.1240.346-0.0799-0.04240.02670.05860.0088-0.027-0.092285.179347.2716.3184
202.82551.62591.61175.40363.5935.07140.0212-0.11650.2098-0.16970.1643-0.5437-0.37010.3987-0.1855-0.1526-0.00430.02730.08980.01550.044398.12759.051319.5287
210.90520.2023-0.01460.7263-0.48061.61370.0044-0.017-0.0658-0.0455-0.0416-0.15260.18930.2760.0372-0.06970.00470.0389-0.0692-0.0005-0.075890.825956.088432.01
221.9403-1.98490.60747.04211.00912.3381-0.0158-0.1479-0.37680.32450.0485-0.01090.4663-0.0533-0.0327-0.0392-0.06860.0461-0.05440.015-0.061477.634948.335231.0209
231.4219-0.11890.6361.08520.05731.7820.0711-0.1491-0.29370.1548-0.0627-0.1360.31350.2151-0.00840.02380.02280.03-0.06950.02-0.01182.984440.211122.8971
240.9481-0.06970.44232.05120.65191.78620.07370.1282-0.191-0.1361-0.00920.05150.18570.2066-0.0645-0.07270.00970.0382-0.0323-0.0019-0.064981.767144.553612.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1221 - 121
2X-RAY DIFFRACTION2AA123 - 151122 - 150
3X-RAY DIFFRACTION3AA152 - 254151 - 253
4X-RAY DIFFRACTION4AA255 - 306254 - 305
5X-RAY DIFFRACTION5AA307 - 455306 - 454
6X-RAY DIFFRACTION6AA456 - 541455 - 540
7X-RAY DIFFRACTION7BB2 - 1191 - 118
8X-RAY DIFFRACTION8BB120 - 151119 - 150
9X-RAY DIFFRACTION9BB152 - 254151 - 253
10X-RAY DIFFRACTION10BB255 - 306254 - 305
11X-RAY DIFFRACTION11BB307 - 514306 - 513
12X-RAY DIFFRACTION12BB515 - 541514 - 540
13X-RAY DIFFRACTION13CC2 - 1261 - 125
14X-RAY DIFFRACTION14CC127 - 151126 - 150
15X-RAY DIFFRACTION15CC152 - 254151 - 253
16X-RAY DIFFRACTION16CC255 - 306254 - 305
17X-RAY DIFFRACTION17CC307 - 454306 - 453
18X-RAY DIFFRACTION18CC455 - 541454 - 540
19X-RAY DIFFRACTION19DD2 - 1221 - 121
20X-RAY DIFFRACTION20DD123 - 151122 - 150
21X-RAY DIFFRACTION21DD152 - 254151 - 253
22X-RAY DIFFRACTION22DD255 - 306254 - 305
23X-RAY DIFFRACTION23DD307 - 454306 - 453
24X-RAY DIFFRACTION24DD455 - 541454 - 540

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