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- PDB-4r84: Crystal structure of Sialyltransferase from Photobacterium damsel... -

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Basic information

Entry
Database: PDB / ID: 4r84
TitleCrystal structure of Sialyltransferase from Photobacterium damsela with CMP-3F(a)Neu5Ac bound
ComponentsSialyltransferase 0160
KeywordsTRANSFERASE / Rossmann Fold / glycosyltransferase GT-B structural group
Function / homology
Function and homology information


negative regulation of phosphate metabolic process / phosphate ion transport / intracellular phosphate ion homeostasis / glycosyltransferase activity / metal ion binding
Similarity search - Function
Immunoglobulin-like - #3010 / Phosphate transport system protein PhoU / PhoU domain / PhoU domain / PhoU-like domain superfamily / Sialyltransferase, C-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 ...Immunoglobulin-like - #3010 / Phosphate transport system protein PhoU / PhoU domain / PhoU domain / PhoU-like domain superfamily / Sialyltransferase, C-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-CSF / Sialyltransferase 0160
Similarity search - Component
Biological speciesPhotobacterium damselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFisher, A.J. / Chen, X. / Li, Y. / Huynh, N.
CitationJournal: Febs Lett. / Year: 2014
Title: Crystal structures of sialyltransferase from Photobacterium damselae.
Authors: Huynh, N. / Li, Y. / Yu, H. / Huang, S. / Lau, K. / Chen, X. / Fisher, A.J.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Sep 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_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_label_asym_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 / _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_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: Sialyltransferase 0160
B: Sialyltransferase 0160
C: Sialyltransferase 0160
D: Sialyltransferase 0160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,01912
Polymers227,3294
Non-polymers2,6908
Water43,9752441
1
A: Sialyltransferase 0160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5053
Polymers56,8321
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sialyltransferase 0160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5053
Polymers56,8321
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sialyltransferase 0160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5053
Polymers56,8321
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sialyltransferase 0160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5053
Polymers56,8321
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.340, 81.450, 111.210
Angle α, β, γ (deg.)99.02, 91.59, 101.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Sialyltransferase 0160


Mass: 56832.145 Da / Num. of mol.: 4 / Fragment: UNP residues 16-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium damselae (bacteria) / Gene: bst / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O66375, beta-galactoside alpha-(2,6)-sialyltransferase
#2: Chemical
ChemComp-CSF / CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID / CMP-3FNEUAC


Type: RNA linking / Mass: 632.442 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H30FN4O16P
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2441 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 6000, 0.2M sodium chloride, 0.1M HEPES, pH 7.0, crystal soaked in 1.25 mM CMP-3F(a)Neu5Ac for 5 hours prior to freezing, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2011 / Details: Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 229782 / Num. obs: 229782 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 8.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.2 / % possible all: 89.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Z4T
Resolution: 1.7→39.749 Å / SU ML: 0.19 / σ(F): 1.97 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 11502 5.01 %
Rwork0.1715 --
obs0.1731 229738 95.64 %
all-229738 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→39.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15164 0 172 2441 17777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715859
X-RAY DIFFRACTIONf_angle_d1.09121680
X-RAY DIFFRACTIONf_dihedral_angle_d13.4865793
X-RAY DIFFRACTIONf_chiral_restr0.0472429
X-RAY DIFFRACTIONf_plane_restr0.0052795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.29692910.26655744X-RAY DIFFRACTION76
1.7193-1.73950.29273610.2546757X-RAY DIFFRACTION88
1.7395-1.76080.26813890.23687230X-RAY DIFFRACTION95
1.7608-1.78310.27813890.23137199X-RAY DIFFRACTION95
1.7831-1.80650.26273710.22857265X-RAY DIFFRACTION95
1.8065-1.83130.25473660.22357334X-RAY DIFFRACTION96
1.8313-1.85740.28453810.23227205X-RAY DIFFRACTION95
1.8574-1.88510.26013720.21757340X-RAY DIFFRACTION96
1.8851-1.91460.25553790.21467278X-RAY DIFFRACTION96
1.9146-1.9460.2634000.20147317X-RAY DIFFRACTION96
1.946-1.97950.23683900.19727284X-RAY DIFFRACTION96
1.9795-2.01550.2343720.1957321X-RAY DIFFRACTION96
2.0155-2.05430.22553820.1937331X-RAY DIFFRACTION96
2.0543-2.09620.22654060.18797300X-RAY DIFFRACTION96
2.0962-2.14180.22743700.18517403X-RAY DIFFRACTION97
2.1418-2.19160.22773670.18487357X-RAY DIFFRACTION97
2.1916-2.24640.21714060.18347308X-RAY DIFFRACTION97
2.2464-2.30720.21234070.18197430X-RAY DIFFRACTION97
2.3072-2.37510.24053750.18137360X-RAY DIFFRACTION97
2.3751-2.45170.21514010.18027396X-RAY DIFFRACTION97
2.4517-2.53930.21054030.18057388X-RAY DIFFRACTION97
2.5393-2.6410.22934300.17757393X-RAY DIFFRACTION97
2.641-2.76110.23353790.17937446X-RAY DIFFRACTION98
2.7611-2.90670.20973840.17547460X-RAY DIFFRACTION98
2.9067-3.08870.20384060.16997423X-RAY DIFFRACTION98
3.0887-3.32710.18653740.16317473X-RAY DIFFRACTION98
3.3271-3.66170.16863820.14817477X-RAY DIFFRACTION98
3.6617-4.1910.15324070.13967496X-RAY DIFFRACTION99
4.191-5.27830.14714130.137475X-RAY DIFFRACTION99
5.2783-39.76010.19783490.16577046X-RAY DIFFRACTION92
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)
10.26770.0527-0.23380.5142-0.12050.23940.18570.1605-0.09370.1012-0.5078-0.49540.01380.3474-0.52640.09470.19260.16870.44-0.01090.100146.055215.937571.0995
20.7701-0.1019-0.2890.5491-0.19830.20820.0174-0.0119-0.04170.034-0.06110.06090.01220.0765-00.136-0.00570.01560.1331-0.0310.11625.907611.012696.8757
31.09380.2738-0.18370.21920.0550.34020.06660.11250.1713-0.01050.03540.0657-0.0667-0.05520.02360.18450.00940.01110.1161-0.02110.176710.879313.300797.0824
40.060.0231-0.04130.1393-0.05090.04990.0030.0595-0.11430.07010.03520.14940.0104-0.04630.00030.1802-0.0255-0.00630.2206-0.04430.2484-11.0189-4.717399.3834
50.0742-0.0424-0.06370.08370.07520.1113-0.05190.1652-0.0632-0.03540.0610.06560.0265-0.098800.2168-0.0278-0.02020.1973-0.06070.226-0.1472-4.912394.838
60.05310.036-0.01540.13890.06320.03630.04090.02720.10760.04870.05750.08590.0188-0.05030.00010.18890.0134-0.00190.17970.00470.2576-7.318810.1054102.7723
70.1335-0.02930.0274-0.0009-0.00650.0074-0.243-0.0680.20260.0244-0.07770.05270.03610.0115-0.00950.27010.00190.01980.2926-0.01790.252629.265516.350848.8428
80.73630.0521-0.28790.20510.39760.3332-0.03160.08760.1963-0.04180.00990.00840.0339-0.0989-0.00190.1320.0079-0.01190.22320.05980.213936.56820.981229.9397
90.9635-0.101-0.42070.0845-0.08170.67730.13-0.13250.177-0.00510.11640.0515-0.0612-0.06570.10810.189-0.00560.05770.13720.00450.245160.190727.083222.1915
100.13070.07950.04210.2826-0.2090.24120.0301-0.1175-0.1124-0.0408-0.02390.01570.09060.1088-00.23170.0223-0.00130.17680.02470.215976.78288.577217.0574
110.11980.0471-0.07370.09120.04430.06860.0693-0.18650.1424-0.08030.06710.0874-0.01160.07540.00010.1914-0.03140.01460.2083-0.05270.207778.356524.439116.4556
120.35760.09560.04340.13390.21880.3596-0.0736-0.0814-0.10560.1325-0.14710.08070.1408-0.004-0.0140.2414-0.04970.03350.1550.00520.214670.3643-11.5318-8.8474
130.7621-0.4298-0.06960.73360.50260.4408-0.0471-0.1102-0.0108-0.13510.1075-0.0412-0.0490.0510.00140.1621-0.0323-0.02620.18570.00650.151492.0464-3.2496-34.1549
140.2617-0.1380.10480.3196-0.05370.0588-0.0533-0.0717-0.0827-0.04760.04310.02210.04410.056400.22080.0021-0.00780.1720.03740.1777114.8826-23.4455-34.6135
150.2377-0.0392-0.1390.3779-0.12840.1714-0.043-0.1214-0.0643-0.01960.07630.03890.00810.0125-0.00010.2051-0.0078-0.0270.18450.02310.1887115.5341-19.7867-37.6076
160.06510.049-0.0280.0610.01780.02430.0412-0.23660.1336-0.13130.0080.04560.0103-0.09880.00010.1755-0.0269-00.2754-0.07560.2219122.7074-4.7736-37.949
170.33460.029-0.10080.19380.08150.19-0.032-0.0143-0.1317-0.0872-0.0656-0.11860.01050.0942-0.00010.19370.0450.0520.20680.02460.168885.5634-13.101420.2004
180.13630.06680.1060.0789-0.00290.0829-0.07550.2605-0.1326-0.0793-0.0430.06030.11220.0054-0.00530.19410.03640.03240.2172-0.02570.144465.2276-24.447537.9363
190.24660.03460.03620.1223-0.03480.0839-0.05580.0266-0.15250.0518-0.1722-0.09960.06150.183-0.00540.19820.05450.04530.25230.04550.196973.0884-23.299345.658
200.096-0.07470.0540.2409-0.09760.1632-0.083-0.02070.06830.15570.03080.0219-0.1514-0.0396-0.00010.22160.0606-0.00150.1919-0.00440.189661.3911-11.298851.4253
210.53920.2547-0.17180.1771-0.07560.0603-0.12230.0630.21210.14760.06160.0178-0.1661-0.0816-0.02360.31080.0827-0.05470.1668-0.04030.251257.4758-4.435350.5124
220.34140.07160.00080.4499-0.23170.12270.14950.1084-0.0517-0.22030.11590.17610.1743-0.0880.23910.32040.0239-0.10590.2816-0.06470.128148.1823-30.618332.587
230.0415-0.06330.0520.0163-0.02330.0816-0.1111-0.0358-0.0482-0.09370.11340.1640.0775-0.48630.00140.0552-0.3302-0.37290.65170.25110.322229.0973-34.572146.5043
240.4787-0.1352-0.36560.20350.15820.29520.40770.0121-0.1816-0.14060.1750.21130.4614-0.28560.23850.4038-0.0931-0.17850.2920.0440.265442.5745-35.243839.4153
250.04220.0121-0.02580.07270.00130.01270.07060.02610.06530.02580.09710.05680.0639-0.172-0.00010.24080.0081-0.02820.33790.08220.226836.9626-23.541446.7139
260.02110.0101-0.02860.03350.01560.02870.12320.10490.08410.09840.20370.11510.0538-0.22900.2380.04870.0080.39280.10810.338432.7023-17.637150.2085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 24:98 )A24 - 98
2X-RAY DIFFRACTION2( CHAIN A AND RESID 99:245 )A99 - 245
3X-RAY DIFFRACTION3( CHAIN A AND RESID 246:366 )A246 - 366
4X-RAY DIFFRACTION4( CHAIN A AND RESID 367:404 )A367 - 404
5X-RAY DIFFRACTION5( CHAIN A AND RESID 405:443 )A405 - 443
6X-RAY DIFFRACTION6( CHAIN A AND RESID 444:497 )A444 - 497
7X-RAY DIFFRACTION7( CHAIN B AND RESID 25:52 )B25 - 52
8X-RAY DIFFRACTION8( CHAIN B AND RESID 53:218 )B53 - 218
9X-RAY DIFFRACTION9( CHAIN B AND RESID 219:366 )B219 - 366
10X-RAY DIFFRACTION10( CHAIN B AND RESID 367:443 )B367 - 443
11X-RAY DIFFRACTION11( CHAIN B AND RESID 444:497 )B444 - 497
12X-RAY DIFFRACTION12( CHAIN C AND RESID 24:122 )C24 - 122
13X-RAY DIFFRACTION13( CHAIN C AND RESID 123:313 )C123 - 313
14X-RAY DIFFRACTION14( CHAIN C AND RESID 314:393 )C314 - 393
15X-RAY DIFFRACTION15( CHAIN C AND RESID 394:469 )C394 - 469
16X-RAY DIFFRACTION16( CHAIN C AND RESID 470:497 )C470 - 497
17X-RAY DIFFRACTION17( CHAIN D AND RESID 24:122 )D24 - 122
18X-RAY DIFFRACTION18( CHAIN D AND RESID 123:154 )D123 - 154
19X-RAY DIFFRACTION19( CHAIN D AND RESID 155:198 )D155 - 198
20X-RAY DIFFRACTION20( CHAIN D AND RESID 199:245 )D199 - 245
21X-RAY DIFFRACTION21( CHAIN D AND RESID 246:313 )D246 - 313
22X-RAY DIFFRACTION22( CHAIN D AND RESID 314:363 )D314 - 363
23X-RAY DIFFRACTION23( CHAIN D AND RESID 364:394 )D364 - 394
24X-RAY DIFFRACTION24( CHAIN D AND RESID 395:438 )D395 - 438
25X-RAY DIFFRACTION25( CHAIN D AND RESID 439:469 )D439 - 469
26X-RAY DIFFRACTION26( CHAIN D AND RESID 470:497 )D470 - 497

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