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- PDB-2fvk: Crystal structure of dihydropyrimidinase from Saccharomyces kluyv... -

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Basic information

Entry
Database: PDB / ID: 2fvk
TitleCrystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil
Componentsdihydropyrimidinase
KeywordsHYDROLASE / beta/alpha 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
DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / Dihydropyrimidinase
Similarity search - Component
Biological speciesLachancea kluyveri (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / 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 31, 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 / 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 / _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_asym_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_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)250,28016
Polymers249,3004
Non-polymers98012
Water18,7901043
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14170 Å2
ΔGint-395 kcal/mol
Surface area67110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.130, 71.600, 161.890
Angle α, β, γ (deg.)90.00, 91.40, 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
251A
261B
271C
281D

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
93VALVALTHRTHR2AA152 - 171151 - 170
103VALVALTHRTHR2BB152 - 171151 - 170
113VALVALTHRTHR2CC152 - 171151 - 170
123VALVALTHRTHR2DD152 - 171151 - 170
134ILEILEPROPRO2AA306 - 379305 - 378
144ILEILEPROPRO2BB306 - 379305 - 378
154ILEILEPROPRO2CC306 - 379305 - 378
164ILEILEPROPRO2DD306 - 379305 - 378
175ASNASNTYRTYR2AA382 - 540381 - 539
185ASNASNTYRTYR2BB382 - 540381 - 539
195ASNASNTYRTYR2CC382 - 540381 - 539
205ASNASNTYRTYR2DD382 - 540381 - 539
216PROPROARGARG2AA173 - 292172 - 291
226PROPROARGARG2BB173 - 292172 - 291
236PROPROARGARG2CC173 - 292172 - 291
246PROPROARGARG2DD173 - 292172 - 291
257ZNZNDUCDUC6AE - G601 - 604
267ZNZNDUCDUC6BH - J601 - 604
277ZNZNDUCDUC6CK - M601 - 604
287ZNZNDUCDUC6DN - P601 - 604
Detailsthe content of the asymmetric unit equals the biological assembly, which is a 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: Chemical
ChemComp-DUC / DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / DIHYDROURACIL


Mass: 114.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1043 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.1M ammonium sulfate, 1mM CaCl2, 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: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.4→54.23 Å / Num. all: 80380 / Num. obs: 80380 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 43.1 Å2 / Rsym value: 0.097 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 11234 / Rsym value: 0.329 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2fty
Resolution: 2.4→54.23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.32 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.782 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23352 4085 5.1 %RANDOM
Rwork0.17784 ---
obs0.18064 80363 99.14 %-
all-80363 --
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: 34.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å2-1.87 Å2
2--2.76 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.4→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16594 0 40 1043 17677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02217056
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.96823113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88552129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86124.986726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.297152909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5671560
X-RAY DIFFRACTIONr_chiral_restr0.0780.22561
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212828
X-RAY DIFFRACTIONr_nbd_refined0.1890.28510
X-RAY DIFFRACTIONr_nbtor_refined0.3010.211663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.21330
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.212
X-RAY DIFFRACTIONr_mcbond_it0.2571.510877
X-RAY DIFFRACTIONr_mcangle_it0.458217189
X-RAY DIFFRACTIONr_scbond_it1.01337065
X-RAY DIFFRACTIONr_scangle_it1.5084.55919
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2033tight positional0.030.05
2B2033tight positional0.030.05
3C2033tight positional0.030.05
4D2033tight positional0.030.05
1A1929medium positional0.30.5
2B1929medium positional0.350.5
3C1929medium positional0.390.5
4D1929medium positional0.360.5
1A10loose positional0.175
2B10loose positional0.295
3C10loose positional0.255
4D10loose positional0.255
1A2033tight thermal0.050.5
2B2033tight thermal0.050.5
3C2033tight thermal0.050.5
4D2033tight thermal0.050.5
1A1929medium thermal0.362
2B1929medium thermal0.352
3C1929medium thermal0.362
4D1929medium thermal0.332
1A10loose thermal1.7810
2B10loose thermal1.5910
3C10loose thermal1.6510
4D10loose thermal1.2810
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 288 -
Rwork0.26 5185 -
obs--92.67 %
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)
11.7128-0.03840.35140.7247-0.03741.06320.0113-0.2438-0.07740.1192-0.04680.11720.1633-0.26840.0355-0.0572-0.04320.0709-0.1202-0.0038-0.065246.244554.594576.2517
24.25110.52570.22442.84820.7375.9458-0.12660.50870.5566-0.19160.07590.4549-0.2942-0.21690.0506-0.0872-0.00840.025-0.04660.00350.046834.550770.09659.3064
30.6728-0.10590.04220.90920.46351.00060.00890.0535-0.04370.03-0.06960.24430.0967-0.17760.0606-0.0971-0.02470.0049-0.1149-0.0011-0.081743.231454.988347.775
41.87632.040.22736.9937-1.26881.9451-0.01480.1599-0.2758-0.2902-0.0186-0.16790.45030.15920.0334-0.09510.03810.0157-0.108-0.0362-0.104255.600149.312253.5317
51.22930.39850.30830.98670.18771.65730.0727-0.045-0.27560.0351-0.03080.01060.3417-0.085-0.0418-0.0043-0.01880.0268-0.16410.04-0.03350.785742.412867.6789
61.6631.2277-0.77382.8187-3.64977.79650.06410.02490.15060.2001-0.150.1271-0.68470.01950.0859-0.04970.04570.0199-0.1772-0.0526-0.019947.127572.40959.6299
71.22160.05890.02850.7077-0.15171.1243-0.00550.23250.1034-0.10940.01580.0823-0.1296-0.164-0.0103-0.05020.0253-0.0413-0.08280.0079-0.094749.794363.4133.302
81.81410.4289-0.92632.4628-0.97754.1199-0.0833-0.0468-0.22780.04070.09620.29780.3329-0.4006-0.0129-0.13690.0646-0.04470.0257-0.0130.006135.941254.734518.0703
90.71470.0296-0.14510.45180.25030.90230.0007-0.06410.0134-0.0234-0.03230.1596-0.106-0.18030.0317-0.09450.0321-0.0017-0.09980.0094-0.085242.80560.715129.9683
101.922-1.5682-0.43738.5956-1.42312.61740.0012-0.02460.21340.3879-0.042-0.045-0.48840.06880.0408-0.0935-0.02880.0003-0.1071-0.0357-0.132156.245868.466127.6776
111.2733-0.4945-0.28280.99530.24781.58560.03010.04170.2525-0.03130.0024-0.0021-0.3547-0.0397-0.0324-0.00460.0042-0.0194-0.1270.0394-0.047352.208675.350813.2803
121.1914-0.78570.4723.3776-3.8846.98870.13910.0704-0.2416-0.0825-0.1010.27950.5130.1339-0.0381-0.0569-0.0052-0.0067-0.1073-0.066-0.040548.258245.321821.1073
132.2639-0.1848-0.45980.96990.22311.10720.0068-0.20710.06270.06460.0455-0.1341-0.09160.2666-0.0523-0.0575-0.0488-0.0386-0.10540.003-0.112685.386868.986573.7805
140.9121-0.097-0.14030.15840.01261.36150.05010.0820.04920.01020.0043-0.1847-0.20950.2562-0.0544-0.0775-0.04960.0132-0.0995-0.0064-0.07989.414463.144251.0396
152.26852.3145-0.48.7007-0.26562.48710.00250.23230.2156-0.406-0.03170.1212-0.4684-0.01960.0292-0.06730.01570.0069-0.10320.0267-0.138875.797670.442451.9383
161.96970.9044-0.19162.11650.1462.02190.05660.30220.5338-0.28190.00340.0536-0.60950.199-0.060.1623-0.05270.0511-0.09290.06280.050384.225583.460254.0866
171.19280.0502-0.13971.25150.29761.54740.02310.06120.1032-0.0393-0.0114-0.0973-0.23790.0625-0.0116-0.0505-0.04280.0014-0.1660.022-0.096277.917774.26765.8701
180.8681-0.135-0.27381.89840.76471.9024-0.0016-0.13490.11380.09530.03140.076-0.23440.1122-0.0298-0.1269-0.04390.0038-0.12970.0213-0.055679.58374.137270.4858
192.03660.04990.7910.73920.23011.41340.06620.2964-0.1277-0.08990.025-0.11340.19490.2986-0.0913-0.03690.07020.0217-0.0004-0.0179-0.079584.99246.52545.9512
200.9099-0.75370.17092.36060.33772.1275-0.1119-0.00850.3137-0.07050.1264-0.4842-0.48190.4591-0.0145-0.0985-0.01160.01570.1274-0.04260.050897.143959.650821.2095
210.7706-0.0039-0.01090.4253-0.09371.7146-0.0046-0.0305-0.02120.0016-0.0524-0.17880.11760.21370.057-0.10840.0229-0.0135-0.0443-0.0139-0.078990.13155.150531.6817
222.224-2.5950.28111.17740.69782.19510.0268-0.175-0.31170.5961-0.12580.13670.37050.03430.099-0.0938-0.0128-0.0124-0.03750.0205-0.096776.835247.010730.5576
231.3955-0.36320.43610.94080.17622.25550.0811-0.081-0.30440.08220.0161-0.06890.46270.104-0.09720.03660.0276-0.0342-0.0954-0.0017-0.013881.609737.105418.0136
240.9454-1.1499-1.1515.18775.05386.48970.06220.13250.2459-0.2864-0.0974-0.0123-0.59730.04490.0352-0.0125-0.02-0.0039-0.02380.0558-0.037685.011669.250320.3402
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1391 - 138
2X-RAY DIFFRACTION2AA140 - 167139 - 166
3X-RAY DIFFRACTION3AA168 - 254167 - 253
4X-RAY DIFFRACTION4AA255 - 306254 - 305
5X-RAY DIFFRACTION5AA307 - 513306 - 512
6X-RAY DIFFRACTION6AA514 - 541513 - 540
7X-RAY DIFFRACTION7BB2 - 1221 - 121
8X-RAY DIFFRACTION8BB123 - 151122 - 150
9X-RAY DIFFRACTION9BB152 - 254151 - 253
10X-RAY DIFFRACTION10BB255 - 306254 - 305
11X-RAY DIFFRACTION11BB307 - 513306 - 512
12X-RAY DIFFRACTION12BB514 - 541513 - 540
13X-RAY DIFFRACTION13CC2 - 1511 - 150
14X-RAY DIFFRACTION14CC152 - 254151 - 253
15X-RAY DIFFRACTION15CC255 - 306254 - 305
16X-RAY DIFFRACTION16CC307 - 379306 - 378
17X-RAY DIFFRACTION17CC380 - 455379 - 454
18X-RAY DIFFRACTION18CC456 - 541455 - 540
19X-RAY DIFFRACTION19DD2 - 1251 - 124
20X-RAY DIFFRACTION20DD126 - 150125 - 149
21X-RAY DIFFRACTION21DD151 - 254150 - 253
22X-RAY DIFFRACTION22DD255 - 306254 - 305
23X-RAY DIFFRACTION23DD307 - 514306 - 513
24X-RAY DIFFRACTION24DD515 - 542514 - 541

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