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- PDB-4efq: Bombyx mori lipoprotein 7 - platinum derivative at 1.94 A resolution -

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Basic information

Entry
Database: PDB / ID: 4efq
TitleBombyx mori lipoprotein 7 - platinum derivative at 1.94 A resolution
Components30kDa protein
KeywordsUNKNOWN FUNCTION / VHS domain / beta-trefoil
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Lepidopteran low molecular weight (30 kD) lipoprotein, N-terminal domain / Lepidopteran low molecular weight lipoprotein / Lepidopteran low molecular weight lipoprotein, N-terminal domain / Lepidopteran low molecular weight (30 kD) lipoprotein / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / : / THIOCYANATE ION / 30K protein 2
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsPietrzyk, A.J. / Panjikar, S. / Bujacz, A. / Mueller-Dieckmann, J. / Jaskolski, M. / Bujacz, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: High-resolution structure of Bombyx mori lipoprotein 7: crystallographic determination of the identity of the protein and its potential role in detoxification.
Authors: Pietrzyk, A.J. / Panjikar, S. / Bujacz, A. / Mueller-Dieckmann, J. / Lochynska, M. / Jaskolski, M. / Bujacz, G.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_alt_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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 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: 30kDa protein
B: 30kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,56213
Polymers55,1582
Non-polymers1,40411
Water4,161231
1
A: 30kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3017
Polymers27,5791
Non-polymers7226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 30kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2626
Polymers27,5791
Non-polymers6825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.806, 49.785, 54.958
Angle α, β, γ (deg.)93.17, 94.87, 102.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 30kDa protein


Mass: 27579.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: protein isolated from fifth instar larvae / Source: (natural) Bombyx mori (domestic silkworm) / References: UniProt: E5EVW2
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Pt
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES buffer, 22% PEG 3350, 200 mM KSCN, 2.0 mM K2PtCl6, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.071 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2010
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 1.94→54.6 Å / Num. all: 29990 / Num. obs: 29990 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 25.2
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 4.98 / % possible all: 75

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Processing

Software
NameVersionClassification
HKL-2000data collection
Auto-RickshawMR protocolphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EFP
Resolution: 1.94→54.6 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.326 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22665 1019 3.4 %RANDOM
Rwork0.18534 ---
obs0.18675 28971 94.08 %-
all-29990 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.057 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-1.09 Å22.04 Å2
2---1.22 Å2-0.17 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.94→54.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 15 231 4082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223974
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.955382
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69324.455202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3115694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1781522
X-RAY DIFFRACTIONr_chiral_restr0.130.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023054
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9521.52355
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42623789
X-RAY DIFFRACTIONr_scbond_it2.51231619
X-RAY DIFFRACTIONr_scangle_it3.4224.51586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.988 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 62 -
Rwork0.146 1631 -
obs--71.43 %
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)
13.6589-1.2037-3.011211.61921.3932.7710.1141-0.0707-0.3036-0.5028-0.1875-0.70220.09150.14050.07340.17630.0495-0.06930.178-0.00470.213343.0586-6.189119.9452
22.98830.35861.06014.87630.45756.2086-0.0398-0.00710.1884-0.18810.0054-0.3377-0.0826-0.00230.03450.0112-0.01610.00830.080.01380.041538.41474.553722.9091
30.4763-0.17431.31915.28392.67385.56550.01610.04210.0354-0.49930.0479-0.3077-0.29130.1317-0.0640.0759-0.0052-0.01160.11880.01340.07732.9966-6.460316.0115
42.555-0.5780.34013.526-0.48372.96-0.1301-0.2040.0420.32510.0861-0.20120.1720.19710.04410.05530.0322-0.03250.06690.00850.059835.3999-3.821632.1261
52.9587-1.09611.4010.67870.55124.9314-0.0838-0.00880.0839-0.02850.0035-0.0357-0.2701-0.04980.08040.0594-0.0162-0.01670.022-0.01760.061330.83746.175627.1906
60.68080.5853-0.59363.1557-0.00433.4189-0.1060.08240.0355-0.38050.0610.1004-0.0475-0.3840.0450.07670.0087-0.04490.0735-0.00650.042724.76531.149321.8455
72.647-0.8378-0.32222.11280.30693.8965-0.07680.4101-0.127-0.0337-0.09450.22160.1541-0.45410.17140.0601-0.0281-0.03910.1077-0.03150.064618.19772.61231.832
83.5509-1.1726-1.1490.64580.47172.9924-0.0784-0.0760.07270.2410.0361-0.06640.1286-0.09830.04220.1827-0.0145-0.03090.14130.00040.059814.34125.254949.0717
97.43960.4790.578310.3759-0.99324.0834-0.0046-0.0337-0.16670.4358-0.1106-0.19070.1092-0.21740.11520.0471-0.01330.0030.116-0.0010.011710.98117.588650.3776
104.45621.5992-1.78591.9965-0.44072.1308-0.09030.1394-0.1196-0.02940.04040.11590.146-0.32980.04990.08350.0011-0.04050.1085-0.00360.048315.33747.669737.401
1110.40112.8867-4.99041.0688-1.26073.8793-0.3464-0.2202-0.0701-0.03330.1198-0.10280.2050.11110.22670.06220.0278-0.05160.1304-0.03950.098229.09513.839833.2702
122.6167-0.14911.5461.71030.59942.4465-0.0901-0.11370.15720.04880.00670.0246-0.2117-0.10450.08340.04740.0155-0.01150.11770.02230.025518.138313.779347.0923
136.0441-4.56372.15464.9071-1.00611.0720.04140.47470.3991-0.4056-0.1554-0.2443-0.2370.25450.1140.3334-0.00850.07170.22120.04790.199316.38919.00444.5757
141.6202-0.6235-0.56370.46-0.1542.6576-0.10670.0227-0.08810.1060.0439-0.03930.2430.04320.06270.08340.0218-0.03670.0819-0.0040.041326.93876.36643.1715
154.2306-1.4955-4.46880.57522.01438.84110.0275-0.3076-0.09110.04760.08020.01260.4396-0.1473-0.10780.1545-0.0263-0.0190.17430.03340.090714.15752.611157.5173
160.87990.5298-0.72122.51061.10492.2204-0.1364-0.0749-0.17370.14920.0875-0.13720.30040.22380.04890.14590.0598-0.03120.10020.01270.07825.3841.058447.033
175.1356-0.1796-1.19563.5006-0.64073.20930.2291-0.14850.30230.2776-0.00160.4577-0.3344-0.1895-0.22740.1350.03690.01250.0558-0.01260.1071-6.805437.495436.628
184.87374.649-1.31645.6511-3.05113.02320.2362-0.3680.36220.3523-0.25160.2673-0.24520.00870.01540.11150.0202-0.010.1395-0.0590.041-5.278529.740844.1106
190.7453-0.6536-2.33592.5642-0.519911.87030.08920.0557-0.0909-0.01310.02090.4286-0.11520.0378-0.11010.05310.0275-0.01290.08090.02370.0874-8.504829.137732.2795
206.7801-2.76814.99913.48670.34937.4303-0.00870.1043-0.0537-0.21950.0440.0809-0.1697-0.1679-0.03540.0468-0.0174-0.01580.09060.01650.0209-2.157132.555425.8993
213.88771.99280.49986.4551-2.15813.59350.0582-0.1967-0.24960.2006-0.0444-0.3776-0.16290.2497-0.01380.0272-0.0025-0.01440.0710.00190.03615.431227.243638.0811
221.4889-0.8732-1.18210.57591.0934.5416-0.1265-0.03970.01460.09670.0578-0.0070.18250.06170.06870.05130.0082-0.02640.04920.0050.03672.81919.466631.5058
233.2769-1.00070.31221.1170.17372.4175-0.11440.1985-0.21720.03150.02920.17050.0293-0.08650.08520.0622-0.0132-0.02240.0814-0.00240.04664.303116.041612.2738
248.394-0.5196-1.751212.6783.8028.07120.0711-0.0610.4276-0.22540.0079-1.0356-0.52020.4884-0.07890.14230.0289-0.01120.18040.03010.138922.081315.32828.6342
250.3336-0.1276-0.45233.14620.88561.86050.01210.0485-0.04060.10240.0232-0.06250.2502-0.0131-0.03530.06820.0161-0.04150.10650.00330.059410.947316.501819.3338
264.6828-2.9413-2.70325.48680.39352.03230.19370.0709-0.0318-0.2594-0.1610.2427-0.07010.0038-0.03270.09180.0022-0.06330.09070.00740.123710.620833.869427.0823
276.0243-1.1344-2.95265.0986-0.38471.6321-0.1292-0.2669-0.24950.0072-0.057-0.260.08690.17440.18620.09840.056-0.05240.146-0.00080.06817.835817.367819.6872
284.0981-0.91620.0966.3863-0.75033.0244-0.04450.17610.1068-0.1156-0.0261-0.0565-0.10410.24540.07070.0752-0.0092-0.01250.1489-0.0260.027116.15427.14458.4046
297.98261.0936-3.9454.21280.43913.03960.165-0.0385-0.27070.1023-0.0615-0.2791-0.07090.2116-0.10340.0772-0.0064-0.03560.1227-0.01530.077814.74730.345318.8568
306.58783.04561.10444.40111.5091.53230.08670.1991-0.43680.1337-0.03460.15430.3267-0.3793-0.05220.2047-0.0319-0.02310.3487-0.03450.1995-6.591724.067420.3871
310.3943-0.153-0.14231.07370.50691.3951-0.02730.13110.04-0.1007-0.0180.1361-0.0654-0.0630.04530.03830.0078-0.03340.09520.00640.03536.298624.67579.7414
320.7759-0.0174-0.99674.69780.3872.52030.05230.0682-0.0479-0.2209-0.2220.1339-0.0856-0.07850.16970.0276-0.0077-0.02260.1259-0.00760.0325-0.627922.142815.4705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 14
2X-RAY DIFFRACTION2A15 - 31
3X-RAY DIFFRACTION3A32 - 42
4X-RAY DIFFRACTION4A43 - 55
5X-RAY DIFFRACTION5A56 - 64
6X-RAY DIFFRACTION6A65 - 79
7X-RAY DIFFRACTION7A80 - 92
8X-RAY DIFFRACTION8A93 - 110
9X-RAY DIFFRACTION9A111 - 120
10X-RAY DIFFRACTION10A121 - 136
11X-RAY DIFFRACTION11A137 - 143
12X-RAY DIFFRACTION12A144 - 166
13X-RAY DIFFRACTION13A167 - 174
14X-RAY DIFFRACTION14A175 - 208
15X-RAY DIFFRACTION15A209 - 218
16X-RAY DIFFRACTION16A219 - 239
17X-RAY DIFFRACTION17B5 - 24
18X-RAY DIFFRACTION18B25 - 40
19X-RAY DIFFRACTION19B41 - 50
20X-RAY DIFFRACTION20B51 - 59
21X-RAY DIFFRACTION21B60 - 71
22X-RAY DIFFRACTION22B72 - 91
23X-RAY DIFFRACTION23B92 - 104
24X-RAY DIFFRACTION24B105 - 114
25X-RAY DIFFRACTION25B115 - 136
26X-RAY DIFFRACTION26B137 - 142
27X-RAY DIFFRACTION27B143 - 153
28X-RAY DIFFRACTION28B154 - 173
29X-RAY DIFFRACTION29B174 - 182
30X-RAY DIFFRACTION30B183 - 190
31X-RAY DIFFRACTION31B191 - 224
32X-RAY DIFFRACTION32B225 - 239

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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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