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- PDB-4muy: IspH in complex with pyridin-4-ylmethyl diphosphate -

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Basic information

Entry
Database: PDB / ID: 4muy
TitleIspH in complex with pyridin-4-ylmethyl diphosphate
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / Iron-sulfur protein / Reductase / pyridin-4-ylmethyl diphosphate / Cytosol
Function / homology4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain / Rossmann fold - #11270 / Cobalt-precorrin-4 Transmethylase; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / pyridin-4-ylmethyl trihydrogen diphosphate / FE3-S4 CLUSTER / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSpan, I. / Wang, K. / Song, Y. / Eisenreich, W. / Bacher, A. / Oldfield, E. / Groll, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Insights into the Binding of Pyridines to the Iron-Sulfur Enzyme IspH.
Authors: Span, I. / Wang, K. / Eisenreich, W. / Bacher, A. / Zhang, Y. / Oldfield, E. / Groll, M.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Sep 20, 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_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_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3466
Polymers72,2162
Non-polymers1,1304
Water9,710539
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6733
Polymers36,1081
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6733
Polymers36,1081
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.190, 80.460, 110.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999605, -0.008808, 0.026682), (-0.009182, 0.999861, -0.013925), (-0.026556, -0.014165, -0.999547)-4.31641, 0.08889, -0.00479

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Components

#1: Protein 4-hydroxy-3-methylbut-2-enyl diphosphate reductase


Mass: 36107.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: ECDH1ME8569_0026, ispH / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue
References: UniProt: C9QSC3, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-2E5 / pyridin-4-ylmethyl trihydrogen diphosphate


Mass: 269.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS, 0.2 M ammonium sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012
RadiationMonochromator: double-crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 58881 / Num. obs: 58292 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 0.088 / Net I/σ(I): 8.92
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 2.81 / Rsym value: 0.416 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8
Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.986 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 2915 5 %RANDOM
Rwork0.1771 ---
all0.17941 55952 --
obs0.17941 55376 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.303 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---3.47 Å20 Å2
3---2.57 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 46 539 5358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194895
X-RAY DIFFRACTIONr_bond_other_d0.0020.024751
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9766636
X-RAY DIFFRACTIONr_angle_other_deg0.764310900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69824.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35815853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6941544
X-RAY DIFFRACTIONr_chiral_restr0.0830.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021075
X-RAY DIFFRACTIONr_rigid_bond_restr2.55539646
X-RAY DIFFRACTIONr_sphericity_free37.1275147
X-RAY DIFFRACTIONr_sphericity_bonded10.93359964
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 207 -
Rwork0.236 3940 -
obs--99.74 %
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)
16.78281.6143-1.01560.468-0.36780.3459-0.0190.09570.0857-0.01530.05670.05250.0186-0.0649-0.03770.1533-0.00280.00220.1634-0.01120.1172-28.0898-8.75567.5683
23.597-1.46940.61321.0492-0.42180.34250.03270.0032-0.17820.02890.00110.01390.07690.0201-0.03380.1425-0.0001-0.00740.1445-0.00080.0458-5.5312-9.76311.0077
30.83930.07990.34821.7808-0.12910.82660.0094-0.0992-0.03730.1111-0.0239-0.13340.04320.04380.01440.14450.0002-0.01580.16370.01960.0874.7132-13.10421.8031
42.3993-0.42360.42080.789-0.1911.4970.033-0.0138-0.0560.0631-0.01440.18260.0331-0.0336-0.01860.1528-0.0017-0.00050.15430.00130.0546-8.4009-9.958421.497
52.50010.71921.28051.7619-0.59691.25850.0386-0.04280.070.2532-0.08280.0335-0.11750.03790.04420.2005-0.01090.01160.19470.01040.07082.1022-9.276527.6972
60.20470.00570.2320.22910.20280.44460.0460.0164-0.05190.02420.0228-0.05460.0280.0569-0.06880.1766-0.0119-0.02310.19580.03350.12845.7798-4.910120.809
70.48890.4348-0.98333.4917-0.99171.9850.0341-0.016-0.02680.1074-0.1046-0.4834-0.09910.04430.07050.1639-0.0059-0.03950.18260.00730.126312.83240.255222.6241
80.45850.2931-0.20150.2047-0.04490.563-0.0329-0.0254-0.0879-0.0325-0.0077-0.0670.03960.05780.04060.1663-00.00830.17010.00770.09163.4576-0.24411.6291
91.7280.5998-0.54334.79731.3031.3421-0.05560.06230.0492-0.1385-0.0142-0.41160.0070.07010.06990.158-0.0048-0.00380.17370.02230.11978.638815.05719.0669
100.18420.1246-0.34212.4308-0.83730.79270.010.0031-0.00710.1099-0.041-0.0761-0.0495-0.00580.0310.1591-0.0051-0.00620.164-0.00290.0739-4.458212.295217.2487
110.4054-0.485-0.01231.4128-0.1340.0857-0.0157-0.03420.07030.0814-0.0019-0.0757-0.04720.04190.01770.162-0.0091-0.00920.1653-0.00530.0811-0.810821.173716.2471
120.3788-0.0609-0.16912.062-0.33740.4772-0.0089-0.00220.06120.04230.03220.1242-0.0312-0.0132-0.02330.1506-0.0029-0.00090.14620.00240.0621-10.603214.307510.0863
130.3276-0.2532-0.09881.48550.88940.5442-0.01340.01080.0225-0.0236-0.02160.0427-0.0080.00240.0350.16770.00030.00340.16520.00380.0787-5.969222.76435.1728
141.17130.31530.2910.41890.46820.5457-0.010.10850.1011-0.0148-0.00860.0558-0.0086-0.02610.01850.13860.0008-0.00450.14720.01030.089-16.12452.74775.8475
151.62280.08040.10180.9408-0.19640.1956-0.0275-0.06590.06280.0738-0.01170.15360.0082-0.02510.03930.1543-0.00170.00150.1569-0.01550.0651-23.79450.416115.5683
161.41730.0530.02591.10860.23082.3599-0.0117-0.1649-0.0060.1299-0.0130.2120.047-0.17680.02470.1325-0.0107-0.02450.1541-0.00110.0713-32.822-8.561120.185
172.0731.066-0.15170.94040.09130.29260.00750.0009-0.12720.0145-0.02310.03320.0442-0.01820.01570.14870.00070.00240.1532-0.00350.0679-20.4935-11.572113.5861
181.42871.1411-1.46591.4039-2.04223.2472-0.06340.03840.032-0.06560.04560.03010.2306-0.01440.01780.14740.0119-0.00880.1339-0.02090.0955-27.652-11.58777.8703
193.09020.51221.61630.09630.31651.06030.03930.0883-0.10160.01150.0199-0.01420.06320.0634-0.05930.1653-0.00710.00280.16220.00270.0601-3.4143-7.44742.338
2013.67482.0602-7.74660.456-0.80865.7006-0.22750.19160.2447-0.0740.00770.03020.0535-0.03950.21980.14990.02840.00330.22270.09830.3249.0388-13.38018.1239
215.0322-0.5916-0.98650.13070.2060.3313-0.007-0.1083-0.01060.02450.0353-0.03630.03110.0573-0.02830.15970.0123-0.00060.16840.00880.121723.5106-8.8609-8.024
220.75330.3310.1790.52810.30140.44150.00120.0368-0.038-0.0436-0.02630.0050.0612-0.01420.02510.14740.0032-0.00430.1513-0.00240.061-1.4426-11.1789-17.5783
235.1875-2.75431.98941.4639-1.01143.78790.0013-0.15250.00410.0130.1141-0.00450.2374-0.0341-0.11540.18290.0024-0.00760.2001-0.02350.064-1.265-17.8181-25.304
240.05360.09540.10330.25060.1720.20750.0020.00070.0178-0.0569-0.02550.05030.0192-0.02670.02350.16980.0008-0.00350.175-0.00510.0824-10.3277-6.3653-24.5526
252.52342.6493-0.17372.99120.23550.851-0.1275-0.00780.1576-0.0966-0.03870.26320.0328-0.04870.16620.17880.01620.00530.1711-0.00540.1227-16.59342.2137-20.2938
261.62160.6541.22080.4230.3631.1085-0.0108-0.06080.0213-0.0007-0.00910.08940.0069-0.08050.01990.15550.00150.0020.1652-0.00540.098-11.679-4.1712-15.7263
274.0177-2.0053-0.6555.2049-0.69830.36540.0302-0.24790.17490.18320.03720.1881-0.0310.0476-0.06740.1582-0.00590.01940.1647-0.03570.1276-11.214811.8286-8.6554
280.19910.3899-0.10731.04340.00850.23070.01790.01220.0167-0.037-0.0290.0571-0.0558-0.03260.01110.16170.0098-0.00510.1660.00180.0877-1.742213.2227-16.7576
291.4945-2.342-0.00725.1305-0.53490.22120.05140.14320.0134-0.0587-0.00810.1708-0.0305-0.0569-0.04330.16560.0054-0.01210.18190.00940.1012-11.143914.8206-17.9374
300.11030.0562-0.11111.18140.15490.32430.02060.02440.0571-0.0481-0.00260.001-0.0557-0.0108-0.01810.15880.00510.00570.15220.00420.07872.002519.6987-13.496
310.5594-0.55010.5221.3293-1.17981.0621-0.028-0.0078-0.00050.0397-0.0208-0.0828-0.0461-0.02040.04890.15920.00150.00230.173-0.00270.08581.197322.7399-5.3055
320.29870.2106-0.10960.7435-0.75620.81840.0128-0.09810.02350.0235-0.0238-0.0005-0.01420.00360.0110.1374-0.0027-0.00250.1383-0.00440.05159.24732.9881-6.2163
332.3277-1.1371-2.96512.03190.61594.38660.0812-0.18470.1413-0.11270.0881-0.0891-0.00930.0995-0.16930.1416-0.0138-0.00660.16840.00410.10824.88660.0558-8.0574
341.88420.7977-0.29891.4310.41870.34780.00470.10450.0647-0.10860.0211-0.0964-0.0176-0.0001-0.02580.16480.00830.02460.1670.02090.093914.4334-0.013-17.1868
350.57830.1704-0.03392.82730.8830.5152-0.02590.06690.1279-0.0460.0186-0.03960.01040.04470.00730.14840.00210.01110.16510.01090.078121.7499-0.1128-17.7254
362.61020.14851.13661.30780.36272.771-0.02570.24540.0204-0.08390.0187-0.19660.0110.16030.0070.1615-0.00240.01140.14860.0130.076728.9086-8.6564-20.6984
370.6949-0.9532-0.08231.31250.10120.05880.005-0.0021-0.0219-0.0115-0.00090.01830.02190.0173-0.00410.1498-0.002-0.00090.153-0.00310.090615.8118-11.6371-13.8479
381.6511-1.5372-1.84331.89361.9743.1154-0.1184-0.0695-0.03130.04010.0296-0.03880.14990.08360.08880.1471-0.008-0.01640.14710.02350.088622.9846-11.7078-8.2966
395.02090.93142.23940.18660.36931.17870.0221-0.0845-0.0568-0.0114-0.019-0.02610.1046-0.0762-0.00310.16340.0053-0.01330.1619-0.00020.0647-2.0694-7.7974-3.1256
4012.71456.39285.18299.70735.084611.4436-0.092-0.35790.43390.5957-0.81930.40140.6317-0.47790.91130.2374-0.00230.04210.1973-0.02540.075-12.3754-15.6408-7.5751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 24
3X-RAY DIFFRACTION3A25 - 37
4X-RAY DIFFRACTION4A38 - 49
5X-RAY DIFFRACTION5A50 - 64
6X-RAY DIFFRACTION6A65 - 77
7X-RAY DIFFRACTION7A78 - 89
8X-RAY DIFFRACTION8A90 - 103
9X-RAY DIFFRACTION9A104 - 114
10X-RAY DIFFRACTION10A115 - 127
11X-RAY DIFFRACTION11A128 - 162
12X-RAY DIFFRACTION12A163 - 181
13X-RAY DIFFRACTION13A182 - 193
14X-RAY DIFFRACTION14A194 - 210
15X-RAY DIFFRACTION15A211 - 246
16X-RAY DIFFRACTION16A247 - 261
17X-RAY DIFFRACTION17A262 - 280
18X-RAY DIFFRACTION18A281 - 297
19X-RAY DIFFRACTION19A298 - 304
20X-RAY DIFFRACTION20A305 - 309
21X-RAY DIFFRACTION21B1 - 7
22X-RAY DIFFRACTION22B8 - 49
23X-RAY DIFFRACTION23B50 - 54
24X-RAY DIFFRACTION24B55 - 76
25X-RAY DIFFRACTION25B77 - 86
26X-RAY DIFFRACTION26B87 - 100
27X-RAY DIFFRACTION27B101 - 112
28X-RAY DIFFRACTION28B113 - 127
29X-RAY DIFFRACTION29B128 - 140
30X-RAY DIFFRACTION30B141 - 181
31X-RAY DIFFRACTION31B182 - 193
32X-RAY DIFFRACTION32B194 - 207
33X-RAY DIFFRACTION33B208 - 216
34X-RAY DIFFRACTION34B217 - 235
35X-RAY DIFFRACTION35B236 - 248
36X-RAY DIFFRACTION36B249 - 261
37X-RAY DIFFRACTION37B262 - 280
38X-RAY DIFFRACTION38B281 - 297
39X-RAY DIFFRACTION39B298 - 305
40X-RAY DIFFRACTION40B306 - 310

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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