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Basic information

Entry
Database: PDB / ID: 6rkc
TitleInter-dimeric interface controls function and stability of S-methionine adenosyltransferase from U. urealiticum
ComponentsMethionine adenosyltransferase
KeywordsTRANSFERASE / synthetase
Function / homologyGMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / : / (DIPHOSPHONO)AMINOPHOSPHONIC ACID / S-ADENOSYLMETHIONINE / :
Function and homology information
Biological speciesUreaplasma urealyticum serovar 7 str. ATCC 27819 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsShahar, A. / Zarivach, R. / Bershtein, S. / Kleiner, D. / Shmulevich, F.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1630/15 Israel
CitationJournal: J.Mol.Biol. / Year: 2019
Title: The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase.
Authors: Kleiner, D. / Shmulevich, F. / Zarivach, R. / Shahar, A. / Sharon, M. / Ben-Nissan, G. / Bershtein, S.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: 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 / refine / refine_hist / struct_conn / struct_ncs_dom_lim
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_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_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_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 / _refine.pdbx_diffrn_id / _refine_hist.d_res_low / _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_conn.ptnr2_label_seq_id / _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: Methionine adenosyltransferase
B: Methionine adenosyltransferase
C: Methionine adenosyltransferase
D: Methionine adenosyltransferase
E: Methionine adenosyltransferase
F: Methionine adenosyltransferase
G: Methionine adenosyltransferase
H: Methionine adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,13855
Polymers343,0458
Non-polymers9,09347
Water2,216123
1
A: Methionine adenosyltransferase
B: Methionine adenosyltransferase
C: Methionine adenosyltransferase
D: Methionine adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,05027
Polymers171,5224
Non-polymers4,52723
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19700 Å2
ΔGint-141 kcal/mol
Surface area48320 Å2
MethodPISA
2
E: Methionine adenosyltransferase
F: Methionine adenosyltransferase
G: Methionine adenosyltransferase
H: Methionine adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,08928
Polymers171,5224
Non-polymers4,56624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20260 Å2
ΔGint-146 kcal/mol
Surface area47660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.372, 79.467, 143.787
Angle α, β, γ (deg.)90.00, 105.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASNASNAA4 - 3744 - 374
21LYSLYSASNASNBB4 - 3744 - 374
12LYSLYSASNASNAA4 - 3744 - 374
22LYSLYSASNASNCC4 - 3744 - 374
13LYSLYSSERSERAA4 - 3754 - 375
23LYSLYSSERSERDD4 - 3754 - 375
14LYSLYSSERSERAA4 - 3754 - 375
24LYSLYSSERSEREE4 - 3754 - 375
15LYSLYSASNASNAA4 - 3744 - 374
25LYSLYSASNASNFF4 - 3744 - 374
16LYSLYSASNASNAA4 - 3744 - 374
26LYSLYSASNASNGG4 - 3744 - 374
17LYSLYSSERSERAA4 - 3754 - 375
27LYSLYSSERSERHH4 - 3754 - 375
18LYSLYSASNASNBB4 - 3744 - 374
28LYSLYSASNASNCC4 - 3744 - 374
19LYSLYSASNASNBB4 - 3744 - 374
29LYSLYSASNASNDD4 - 3744 - 374
110LYSLYSASNASNBB4 - 3744 - 374
210LYSLYSASNASNEE4 - 3744 - 374
111LYSLYSHISHISBB4 - 3774 - 377
211LYSLYSHISHISFF4 - 3774 - 377
112LYSLYSASNASNBB4 - 3744 - 374
212LYSLYSASNASNGG4 - 3744 - 374
113LYSLYSASNASNBB4 - 3744 - 374
213LYSLYSASNASNHH4 - 3744 - 374
114LYSLYSASNASNCC4 - 3744 - 374
214LYSLYSASNASNDD4 - 3744 - 374
115LYSLYSASNASNCC4 - 3744 - 374
215LYSLYSASNASNEE4 - 3744 - 374
116LYSLYSASNASNCC4 - 3744 - 374
216LYSLYSASNASNFF4 - 3744 - 374
117TYRTYRSERSERCC3 - 3753 - 375
217TYRTYRSERSERGG3 - 3753 - 375
118LYSLYSASNASNCC4 - 3744 - 374
218LYSLYSASNASNHH4 - 3744 - 374
119LYSLYSSERSERDD4 - 3754 - 375
219LYSLYSSERSEREE4 - 3754 - 375
120LYSLYSASNASNDD4 - 3744 - 374
220LYSLYSASNASNFF4 - 3744 - 374
121LYSLYSASNASNDD4 - 3744 - 374
221LYSLYSASNASNGG4 - 3744 - 374
122LYSLYSSERSERDD4 - 3754 - 375
222LYSLYSSERSERHH4 - 3754 - 375
123LYSLYSASNASNEE4 - 3744 - 374
223LYSLYSASNASNFF4 - 3744 - 374
124LYSLYSASNASNEE4 - 3744 - 374
224LYSLYSASNASNGG4 - 3744 - 374
125LYSLYSSERSEREE4 - 3754 - 375
225LYSLYSSERSERHH4 - 3754 - 375
126LYSLYSASNASNFF4 - 3744 - 374
226LYSLYSASNASNGG4 - 3744 - 374
127LYSLYSASNASNFF4 - 3744 - 374
227LYSLYSASNASNHH4 - 3744 - 374
128LYSLYSASNASNGG4 - 3744 - 374
228LYSLYSASNASNHH4 - 3744 - 374

NCS ensembles :
IDDetails
10B, E
1A, B
2A, C
3A, D
4A, E
5A, F
6A, G
7A, H
8B, C
9B, D
11B, F
12B, G
13B, H
14C, D
15C, E
16C, F
17C, G
18C, H
19D, E
20D, F
21D, G
22D, H
23E, F
24E, G
25E, H
26F, G
27F, H
28G, H

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Methionine adenosyltransferase


Mass: 42880.602 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureaplasma urealyticum serovar 7 str. ATCC 27819 (bacteria)
Gene: metK, UUR7_0462 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: B2NE58, methionine adenosyltransferase

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Non-polymers , 5 types, 170 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical
ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID


Mass: 256.970 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: H6NO9P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Mg Formate and 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.55→47.78 Å / Num. obs: 100906 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Net I/σ(I): 5.9
Reflection shellResolution: 2.55→2.6 Å / Rmerge(I) obs: 0.612 / Num. unique obs: 4614 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RJS
Resolution: 2.56→47.78 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.91 / SU B: 52.006 / SU ML: 0.473 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28409 4982 5 %RANDOM
Rwork0.26016 ---
obs0.26136 95107 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.964 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å2-0 Å23.9 Å2
2--0.57 Å20 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.56→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23398 0 559 123 24080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01924388
X-RAY DIFFRACTIONr_bond_other_d0.0020.0222534
X-RAY DIFFRACTIONr_angle_refined_deg2.2151.97533062
X-RAY DIFFRACTIONr_angle_other_deg1.202352521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84552976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35425.6041085
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.334154301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2481580
X-RAY DIFFRACTIONr_chiral_restr0.1540.23767
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0226712
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024656
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_it1.3062.35411970
X-RAY DIFFRACTIONr_mcbond_other1.3062.35411970
X-RAY DIFFRACTIONr_mcangle_it2.1943.52714921
X-RAY DIFFRACTIONr_mcangle_other2.1943.52714922
X-RAY DIFFRACTIONr_scbond_it1.192.46712418
X-RAY DIFFRACTIONr_scbond_other1.192.46712419
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0183.65418141
X-RAY DIFFRACTIONr_long_range_B_refined5.29944.534105203
X-RAY DIFFRACTIONr_long_range_B_other5.29844.523105183
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A246720.07
12B246720.07
21A246880.06
22C246880.06
31A245320.07
32D245320.07
41A240360.11
42E240360.11
51A239520.11
52F239520.11
61A239340.11
62G239340.11
71A238040.11
72H238040.11
81B246620.07
82C246620.07
91B245800.08
92D245800.08
101B240180.11
102E240180.11
111B242280.11
112F242280.11
121B239940.11
122G239940.11
131B238080.11
132H238080.11
141C245520.08
142D245520.08
151C239500.11
152E239500.11
161C239540.11
162F239540.11
171C241260.11
172G241260.11
181C237860.11
182H237860.11
191D238900.12
192E238900.12
201D238220.12
202F238220.12
211D239260.11
212G239260.11
221D238780.11
222H238780.11
231E237200.12
232F237200.12
241E237220.13
242G237220.13
251E235520.12
252H235520.12
261F238100.12
262G238100.12
271F233700.13
272H233700.13
281G234800.12
282H234800.12
LS refinement shellResolution: 2.556→2.622 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 327 -
Rwork0.384 6440 -
obs--91.53 %
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)
10.9639-0.148-0.01850.8931-0.1230.52750.0772-0.0526-0.1009-0.14540.00840.09930.07950.0524-0.08560.65840.001-0.53490.0544-0.00760.438835.0264-18.323546.042
20.83440.0721-0.10570.6766-0.21890.8102-0.0345-0.1041-0.06910.04290.11140.0715-0.0867-0.0161-0.0770.59160.0306-0.43690.1286-0.01070.374638.118-1.016962.0514
31.226-0.06790.00371.0502-0.16620.3447-0.1372-0.06780.0707-0.11220.04180.1649-0.1091-0.00820.09540.76930.0137-0.66890.0159-0.00730.58811.67131.556827.4675
40.8078-0.23010.44540.5291-0.09690.84940.0150.02240.032-0.3062-0.01390.1389-0.00030.1429-0.00110.9342-0.0383-0.6910.0320.02940.529622.7320.20939.8894
50.6748-0.12340.18560.4683-0.12290.07850.03870.029-0.0166-0.01880.01280.02750.05830.0552-0.05150.6297-0.0055-0.49310.6163-0.04670.392253.6121-15.0376-23.2842
60.4470.16110.03520.18690.02940.2977-0.00690.04060.02370.0295-0.00550.0019-0.0131-0.00620.01240.5910.0118-0.4410.6165-0.0340.368356.77162.162-7.2771
70.44930.53520.00091.1041-0.25390.3197-0.0430.02510.07730.04790.05010.0865-0.03590.0289-0.00710.62990.0105-0.50930.5451-0.01530.428430.238234.8665-41.657
80.61160.2047-0.00920.306-0.1380.8635-0.0522-0.0051-0.0364-0.0890.02410.02140.02150.17710.02810.6822-0.0097-0.53410.5710.03590.432341.200223.5458-59.3376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 887
2X-RAY DIFFRACTION2B4 - 889
3X-RAY DIFFRACTION3C3 - 689
4X-RAY DIFFRACTION4D4 - 889
5X-RAY DIFFRACTION5E4 - 887
6X-RAY DIFFRACTION6F4 - 889
7X-RAY DIFFRACTION7G3 - 887
8X-RAY DIFFRACTION8H4 - 888

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