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- PDB-5t6m: Structure of the tryptophan synthase b-subunit from Pyroccus furi... -

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Basic information

Entry
Database: PDB / ID: 5t6m
TitleStructure of the tryptophan synthase b-subunit from Pyroccus furiosus with b-methyltryptophan non-covalently bound
ComponentsTryptophan synthase beta chain 1
KeywordsLYASE / Tryptophan synthase / PLP / non-canonical amino acid
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity
Similarity search - Function
Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(betaS)-beta-methyl-L-tryptophan / PHOSPHATE ION / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBuller, A.R. / van Roye, P. / Arnold, F.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM110851 United States
CitationJournal: Biochemistry / Year: 2016
Title: Tryptophan Synthase Uses an Atypical Mechanism To Achieve Substrate Specificity.
Authors: Buller, A.R. / van Roye, P. / Murciano-Calles, J. / Arnold, F.H.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
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
Revision 1.5Nov 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: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,47713
Polymers175,5404
Non-polymers9379
Water4,071226
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1296
Polymers87,7702
Non-polymers3594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-47 kcal/mol
Surface area25780 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3487
Polymers87,7702
Non-polymers5775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-46 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.819, 107.705, 160.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tryptophan synthase beta chain 1


Mass: 43885.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: trpB1, PF1706 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-78U / (betaS)-beta-methyl-L-tryptophan


Mass: 218.252 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H14N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 15-25% PEG3350, 0.1M HEPES / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2015
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 125283 / % possible obs: 99.4 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.452 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DW3
Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.741 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23768 6510 4.9 %RANDOM
Rwork0.20408 ---
obs0.20571 125283 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.879 Å2
Baniso -1Baniso -2Baniso -3
1-3.23 Å20 Å20 Å2
2---0.6 Å20 Å2
3----2.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11723 0 62 226 12011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912045
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211516
X-RAY DIFFRACTIONr_angle_refined_deg1.181.97416313
X-RAY DIFFRACTIONr_angle_other_deg0.8013.00126420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06651540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6124.049494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.971151950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7531560
X-RAY DIFFRACTIONr_chiral_restr0.0650.21798
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022696
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_it0.7021.9926178
X-RAY DIFFRACTIONr_mcbond_other0.7021.9926178
X-RAY DIFFRACTIONr_mcangle_it1.2132.9797709
X-RAY DIFFRACTIONr_mcangle_other1.2132.987710
X-RAY DIFFRACTIONr_scbond_it0.7752.1135867
X-RAY DIFFRACTIONr_scbond_other0.7752.1145868
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3113.1298604
X-RAY DIFFRACTIONr_long_range_B_refined4.0316.23113411
X-RAY DIFFRACTIONr_long_range_B_other4.0316.23313412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 480 -
Rwork0.372 8990 -
obs--97.9 %
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)
10.62220.80980.84061.68670.99615.0056-0.15760.25760.0334-0.61370.1742-0.1939-0.46880.3616-0.01670.3540.01070.11970.25540.08070.154389.12526.821179.117
20.01140.1056-0.02041.22110.06161.0583-0.0016-0.00650.0141-0.038-0.0112-0.05930.08230.15870.01290.08230.00990.04460.24690.02160.252491.31817.477201.013
31.43991.35321.88762.93670.78483.13290.0092-0.1102-0.0458-0.10270.0198-0.06090.0066-0.1639-0.02890.11690.00340.03130.23070.02070.2275.35725.243197.209
42.97890.95891.88281.75050.64212.3184-0.0251-0.10260.0577-0.0095-0.05780.16090.1866-0.1430.08290.09790.02810.02750.24550.0180.180268.71123.214196.024
50.4899-0.3775-0.11850.3831-0.01540.72040.06950.05820.088-0.167-0.0415-0.0942-0.08010.153-0.0280.2256-0.01860.03780.2440.01680.210887.33623.004189.018
60.0490.0610.1230.4747-0.35691.0284-0.05380.01990.0106-0.31070.0397-0.04580.18820.02360.01420.23140.03130.01980.2364-0.00830.188687.4785.292188.304
70.12150.7834-0.75595.6852-4.01536.7074-0.10830.06290.0922-0.79170.48180.72780.4962-0.7867-0.37350.2716-0.0717-0.1870.35610.03850.216972.1279.679182.539
80.46050.257-0.06041.3511-0.31041.65640.05-0.003-0.0568-0.1781-0.01430.07720.315-0.0842-0.03570.16540.01370.00090.1949-0.00490.194982.7742.768193.849
91.8117-0.999-0.80961.1465-0.12441.46810.01330.0105-0.0076-0.0515-0.0066-0.02950.322-0.2008-0.00680.1956-0.02420.00280.2321-0.02290.163683.5660.357201.469
100.0582-0.15720.08011.00740.35791.3209-0.0089-0.01210.05320.05170.0389-0.07470.1570.1931-0.030.05080.0441-0.00130.29090.00610.224292.45513.42225.683
111.1025-0.72430.04520.7410.63222.5676-0.06460.06910.08130.0871-0.06130.03030.5361-0.05030.12590.23560.01480.02710.1920.02360.192786.1331.575224.183
122.94460.2394-0.35770.02580.11463.554-0.32870.08040.00810.0045-0.02340.01230.7362-0.9150.35210.1895-0.14770.05620.403-0.05360.146272.194.834224.733
131.42130.6434-0.70881.31080.28576.3653-0.1361-0.07530.0275-0.1016-0.07080.03220.2684-0.6440.2070.1132-0.04390.00650.3316-0.01610.15471.7954.837225.237
140.0146-0.0058-0.04780.9111-0.46982.017-0.0122-0.02660.04030.20840.0474-0.08670.4850.303-0.03520.2620.0761-0.02360.29790.00490.179489.1117.97231.255
150.0960.005-0.19280.127-0.452.3562-0.1082-0.08140.03370.0940.0388-0.0977-0.1831-0.09410.06940.23710.0622-0.07640.2986-0.04720.193786.30524.96233.145
160.7397-0.11591.36450.8769-1.03736.63070.131-0.41580.0135-0.04480.1804-0.02580.3081-1.004-0.31150.06610.0120.02460.52040.03410.152571.81319.091236.643
170.56450.03530.17780.1396-0.34842.0721-0.027-0.02430.07270.12310.014-0.0361-0.3159-0.0730.01290.13770.03310.00770.2341-0.01530.216584.33530.144224.69
1812.5209-5.07761.12685.7407-1.01550.9103-0.1031-0.2041-0.01170.05690.19240.1580.0568-0.5628-0.08930.1533-0.0023-0.0160.41270.01460.17169.57321.842215.104
191.8526-0.93290.98470.478-0.62514.7681-0.1067-0.5363-0.16010.07810.270.1039-0.1254-0.7241-0.16330.20240.02810.10610.33280.01370.1466110.34143.183219.798
200.6118-0.2968-0.09910.6607-0.21830.4385-0.03370.0489-0.00180.00830.05080.00230.1066-0.1568-0.01710.1673-0.02460.01510.24570.01870.1869116.83534.601198.58
211.54490.3910.61880.3941-0.64983.76340.0792-0.0781-0.2452-0.0353-0.1033-0.0923-0.22720.12790.02410.1725-0.01340.03440.17690.01860.2348127.51548.894202.048
223.084-0.4546-0.98911.6217-0.63763.1929-0.0185-0.46520.10510.13540.04180.0137-0.48120.366-0.02340.238-0.01110.0450.1892-0.01570.1536124.53853.349211.502
230.8057-0.417-0.37740.70860.73210.7669-0.0429-0.0908-0.09110.2336-0.02790.09590.2348-0.05850.07090.2946-0.03550.03740.22550.05090.1839117.39727.146208.164
249.3293-4.2577-2.5852.38881.344.99660.1108-0.21380.057-0.0066-0.08140.09770.42340.469-0.02930.27070.05030.00630.26320.0090.0774132.57933.65220.673
252.92571.9412-1.27951.3343-0.37856.16730.6111-0.54190.52180.406-0.27910.34990.11781.3664-0.33210.3070.01570.06460.489-0.14440.1795136.23238.355216.769
260.7076-0.0112-0.45670.68180.63810.89110.00640.035-0.07720.15750.0552-0.09340.10070.0322-0.06160.27750.0395-0.02810.19540.02250.1593130.52325.046204.458
270.46870.0208-2.6040.18890.201515.0611-0.0692-0.0719-0.0623-0.1229-0.1699-0.13890.09560.10010.23910.3189-0.0079-0.0280.39230.00640.4039148.63936.093192.25
280.78520.79140.17670.86710.50723.096-0.14910.2586-0.1224-0.23050.1741-0.11250.35420.0145-0.0250.53070.2055-0.00750.3618-0.08140.0256128.54625.293157.402
290.2971-0.68780.17012.325-0.02050.63180.060.0542-0.06280.0417-0.03660.12660.1433-0.2443-0.02340.1396-0.0195-0.00460.3432-0.00520.1642117.39632.977181.076
301.25650.64450.53551.3210.24541.1177-0.11670.0968-0.0237-0.25450.0001-0.0455-0.18040.02490.11650.22020.0409-0.00160.2476-0.00860.1714139.07129.604177.608
311.90852.30180.370232.0813-0.88661.1531-0.15090.08370.3769-0.5690.0997-0.3408-0.12410.38040.05110.27310.0160.06520.44950.01120.1514143.59932.429165.634
320.595-0.6071-0.34730.76970.34271.0130.12510.2378-0.0129-0.2107-0.09880.01180.2116-0.291-0.02630.2167-0.0047-0.01940.3674-0.00190.0991119.55734.039170.072
330.62211.28781.1257.23453.19393.63280.09260.28730.0736-0.34570.0086-0.1512-0.34420.2107-0.10120.32980.06650.13640.33390.09210.0884130.64347.593161.199
341.5819-1.46173.394910.7267-4.55997.53220.15080.47340.1222-0.6738-0.5052-1.16030.28651.05380.35440.53120.07150.36330.7250.12720.31137.56647.165158.698
350.6789-0.1851-0.25490.89980.1072.87330.15070.1310.1953-0.1521-0.0916-0.1887-0.2704-0.1369-0.0590.10.06650.06590.26060.06860.1999122.92148.729173.74
362.6753-0.5155-0.21440.46990.82062.60710.31860.27870.02030.0077-0.1268-0.0835-0.1121-0.147-0.19180.14170.01430.05170.25880.10460.1504119.62449.671181.208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 31
2X-RAY DIFFRACTION2A32 - 102
3X-RAY DIFFRACTION3A103 - 135
4X-RAY DIFFRACTION4A136 - 167
5X-RAY DIFFRACTION5A168 - 212
6X-RAY DIFFRACTION6A213 - 277
7X-RAY DIFFRACTION7A278 - 300
8X-RAY DIFFRACTION8A301 - 352
9X-RAY DIFFRACTION9A353 - 385
10X-RAY DIFFRACTION10B1 - 85
11X-RAY DIFFRACTION11B86 - 122
12X-RAY DIFFRACTION12B123 - 138
13X-RAY DIFFRACTION13B139 - 165
14X-RAY DIFFRACTION14B166 - 212
15X-RAY DIFFRACTION15B213 - 282
16X-RAY DIFFRACTION16B283 - 303
17X-RAY DIFFRACTION17B304 - 374
18X-RAY DIFFRACTION18B375 - 386
19X-RAY DIFFRACTION19C1 - 32
20X-RAY DIFFRACTION20C33 - 104
21X-RAY DIFFRACTION21C105 - 144
22X-RAY DIFFRACTION22C145 - 181
23X-RAY DIFFRACTION23C182 - 254
24X-RAY DIFFRACTION24C255 - 282
25X-RAY DIFFRACTION25C283 - 301
26X-RAY DIFFRACTION26C302 - 382
27X-RAY DIFFRACTION27C383 - 390
28X-RAY DIFFRACTION28D1 - 27
29X-RAY DIFFRACTION29D28 - 89
30X-RAY DIFFRACTION30D90 - 161
31X-RAY DIFFRACTION31D162 - 169
32X-RAY DIFFRACTION32D170 - 253
33X-RAY DIFFRACTION33D254 - 280
34X-RAY DIFFRACTION34D281 - 292
35X-RAY DIFFRACTION35D293 - 355
36X-RAY DIFFRACTION36D356 - 385

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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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