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- PDB-4pzl: The crystal structure of adenylate kinase from Francisella tulare... -

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Basic information

Entry
Database: PDB / ID: 4pzl
TitleThe crystal structure of adenylate kinase from Francisella tularensis subsp. tularensis SCHU S4
ComponentsAdenylate kinase
KeywordsTRANSFERASE / structural genomics / The Center for Structural Genomics of Infectious Dis eases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / ATP binding / cytosol
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Adenylate kinase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of adenylate kinase from Francisella tularensis subsp. tularensis SCHU S4
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.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 / _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: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,68413
Polymers109,1304
Non-polymers5559
Water5,188288
1
A: Adenylate kinase
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7896
Polymers54,5652
Non-polymers2244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-19 kcal/mol
Surface area23010 Å2
MethodPISA
2
C: Adenylate kinase
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8957
Polymers54,5652
Non-polymers3305
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-14 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.022, 65.022, 214.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsIt is predicted that the chain A and B, the chain C and D form dimers respectively.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Adenylate kinase / AK / ATP-AMP transphosphorylase / ATP:AMP phosphotransferase / Adenylate monophosphate kinase


Mass: 27282.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: adk, FTT_1161 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BK21(DE)magic / References: UniProt: Q5NFR4, adenylate kinase

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Non-polymers , 5 types, 297 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M CaCl2, 0.1M Tris, 20% (w/v) PEG4000., pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924, 0.97938
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2014 / Details: mirror
RadiationMonochromator: SI 111 CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979381
ReflectionResolution: 2.1→34.5 Å / Num. all: 59141 / Num. obs: 59141 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.8 % / Biso Wilson estimate: 48.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 30.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2896 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→34.148 Å / SU ML: 0.29 / σ(F): 1.97 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 2985 5.05 %random
Rwork0.1913 ---
all0.1936 59075 --
obs0.1936 59075 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→34.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6800 0 33 288 7121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086929
X-RAY DIFFRACTIONf_angle_d1.0899374
X-RAY DIFFRACTIONf_dihedral_angle_d13.3592574
X-RAY DIFFRACTIONf_chiral_restr0.0751104
X-RAY DIFFRACTIONf_plane_restr0.0051223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0992-2.13360.37261490.28012642X-RAY DIFFRACTION100
2.1336-2.17040.29621340.26172718X-RAY DIFFRACTION100
2.1704-2.20980.31711430.24522636X-RAY DIFFRACTION100
2.2098-2.25230.30971540.2382715X-RAY DIFFRACTION100
2.2523-2.29830.26231310.2192661X-RAY DIFFRACTION100
2.2983-2.34820.29011410.22492668X-RAY DIFFRACTION100
2.3482-2.40280.25121370.22462716X-RAY DIFFRACTION100
2.4028-2.46290.25141270.21762686X-RAY DIFFRACTION100
2.4629-2.52950.2941450.2262667X-RAY DIFFRACTION100
2.5295-2.60390.28691440.22982714X-RAY DIFFRACTION100
2.6039-2.68790.29281520.23512658X-RAY DIFFRACTION100
2.6879-2.78390.28661380.23372656X-RAY DIFFRACTION100
2.7839-2.89530.27281290.22292727X-RAY DIFFRACTION100
2.8953-3.0270.26061610.22032660X-RAY DIFFRACTION100
3.027-3.18650.25541510.21682670X-RAY DIFFRACTION100
3.1865-3.3860.26431440.20832695X-RAY DIFFRACTION100
3.386-3.64720.24781450.19072665X-RAY DIFFRACTION100
3.6472-4.01370.22031300.16882689X-RAY DIFFRACTION100
4.0137-4.59330.19681460.14992688X-RAY DIFFRACTION100
4.5933-5.78250.20361560.16012652X-RAY DIFFRACTION100
5.7825-34.15290.1941280.17422507X-RAY DIFFRACTION93
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)
13.1153-1.62610.40417.0565-2.38392.75730.1063-0.0418-0.08450.62790.3660.3757-0.0651-0.3063-0.46880.320.03530.04050.40460.00990.312961.308227.103714.9731
22.84460.63051.80233.71382.68636.54750.41931.2546-0.2219-0.25390.3408-0.767-0.16670.1965-0.73970.44390.0319-0.09430.8330.01440.437158.961325.5606-7.6561
33.5278-1.2008-1.60633.7691-0.35312.20180.42440.55-0.0844-0.2626-0.29610.5341-0.0164-0.8678-0.12630.30870.0344-0.02840.68640.05790.524551.340226.98564.0841
43.7574-0.3628-3.38131.5022-1.14364.2145-0.0389-0.5822-0.29280.31190.35650.8668-0.3227-0.0612-0.31790.66560.17150.24540.51230.1320.512869.465853.209-2.6405
52.57882.3672-1.32643.3094-2.79982.8650.46320.41860.28990.44980.38610.7826-0.5841-0.7628-0.56640.47260.24970.16060.74560.28651.093546.528142.8784.1152
64.48211.10571.55457.52020.85263.41490.1317-0.38340.69080.49640.1481.6923-0.1817-0.9094-0.45330.51930.10920.18960.69750.07180.741447.34234.073715.3568
76.22071.5624-0.23092.078-0.10696.96280.5368-0.88330.48971.23070.2363-0.3445-0.7150.156-0.55950.57250.180.04550.4191-0.11730.491859.885937.425722.0465
83.63860.5996-1.56141.5796-1.1294.9320.1133-0.1784-0.23440.081-0.23130.12060.4649-0.51240.12020.3799-0.0653-0.01410.2105-0.07320.295172.416317.31736.3305
93.49161.18021.70183.01690.08882.9301-0.0366-0.19920.76740.3683-0.18010.0962-0.5970.21180.24230.4516-0.0552-0.04690.249-0.05890.397480.063937.430911.4439
109.1035-2.0727-4.13612.6859-0.51366.77790.1486-0.22080.3634-0.08390.1807-0.1689-0.24590.4364-0.39460.3376-0.0436-0.0130.2154-0.05930.307877.868924.98659.4856
114.1342-2.0647-1.42244.433-2.61524.60590.141-0.56690.17210.318-0.1677-0.56870.24650.35290.08220.27160.0043-0.02640.169-0.01970.373286.933721.77366.0977
126.9525-4.7576-2.45953.33381.49691.87950.69020.3872-0.3982-1.4471-0.59510.5544-0.0347-0.3278-0.01370.59350.15670.01020.5643-0.0390.503973.574835.2836-16.6793
131.697-1.3713-1.11416.25031.47795.73891.11210.5059-0.2797-1.526-0.91450.6292-0.2617-0.6154-0.18310.84050.2314-0.15830.6426-0.05390.55369.796840.1841-20.3943
145.1529-3.41293.8136.0945-5.2144.66270.02960.51390.5466-0.5113-0.5556-1.07610.13841.09570.57220.36640.02940.09240.4049-0.00510.481690.238527.6113-6.2337
155.8418-1.39660.67436.1844-2.43745.83740.0233-0.1557-0.2227-0.2867-0.1791-0.19140.9780.10660.08130.40240.09150.0240.2218-0.07050.317281.028912.8754-0.3312
164.6746-0.43350.54145.4985-1.23491.58060.02820.2599-0.41180.01910.19840.30580.2688-0.5884-0.23040.2731-0.0483-0.0790.50.01960.228364.43761.336348.4396
171.0081-0.4403-1.59123.0499-3.75059.3377-0.0540.39880.2563-0.21250.20320.1096-0.3817-0.1686-0.18280.3767-0.084-0.08910.51910.05450.385266.116114.785432.1081
181.6302-1.0012-0.75433.1869-1.81462.3779-0.13290.25740.2646-0.47640.2018-0.0455-0.46820.1949-0.0960.3759-0.1325-0.05640.5219-0.03750.360272.288516.529837.0561
191.34490.11320.68533.82861.14823.95550.1085-0.2396-0.07250.032-0.0383-0.1639-0.15020.0826-0.08880.2064-0.01-0.05960.3496-0.01270.221572.12549.162747.5389
208.9574-2.3536.63931.5956-1.84634.8578-0.3469-0.86870.45580.23380.3019-0.54730.2465-0.85590.04490.5923-0.1018-0.11620.5744-0.15440.452668.2082-12.88230.2108
214.8011-0.91593.05932.76520.69655.15140.6574-0.904-0.1180.7236-0.2103-0.27110.34410.2645-0.33230.6616-0.2449-0.16460.6893-0.08190.472763.9757-16.37725.1335
220.89420.1554-0.65785.32744.52955.74140.06170.4852-0.8823-0.20050.4976-0.18840.38880.4418-0.44560.37770.0019-0.10650.6658-0.20630.619981.9347-1.872641.7668
232.40872.63521.28536.13713.1414.17010.1355-0.2429-0.39460.69920.2822-0.11370.62780.0409-0.39540.3876-0.0114-0.1370.46090.05590.341871.5092-0.499655.3028
244.89050.7712.25564.68090.27434.1273-0.1528-0.363-0.2778-0.13820.44590.4922-0.2373-0.9825-0.05960.2911-0.0203-0.11530.66980.14560.40649.200111.743637.0566
256.66980.78161.76653.1759-0.76512.92120.2959-0.4553-1.5063-0.25490.26720.27480.8909-0.6224-0.51790.5168-0.1983-0.18870.75430.21410.833547.5733-4.740541.3688
261.0320.1776-0.4721.86790.34871.1259-0.008-0.859-0.2938-0.1619-0.15761.08330.1295-1.0433-0.48130.2167-0.1873-0.32721.3860.4590.96437.47645.92837.4335
272.51670.55460.39342.69560.18962.057-0.23390.35770.134-0.96580.41570.0728-0.20790.1035-0.20010.7075-0.2691-0.07480.5335-0.0420.481561.91792.849213.9244
281.0052-0.3794-0.15721.1554-0.69020.62670.095-0.6768-0.4963-0.27720.25240.60760.518-1.13220.17710.4631-0.2997-0.45951.01520.23110.875738.48633.420923.7884
290.45381.21320.26843.09050.55792.0902-0.37550.27930.43280.09540.54481.1717-0.4739-1.47350.01050.5110.0658-0.1381.2020.26280.826936.540413.615435.0003
302.3356-2.1047-3.39038.4121.74918.6191-0.023-0.55391.0955-0.31940.80150.8303-1.2826-0.9957-0.57690.54430.1115-0.22830.7390.07990.771547.488822.158734.7764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -9 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 160 )
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 183 )
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 217 )
8X-RAY DIFFRACTION8chain 'B' and (resid -9 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 73 )
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 89 )
11X-RAY DIFFRACTION11chain 'B' and (resid 90 through 112 )
12X-RAY DIFFRACTION12chain 'B' and (resid 113 through 134 )
13X-RAY DIFFRACTION13chain 'B' and (resid 135 through 160 )
14X-RAY DIFFRACTION14chain 'B' and (resid 161 through 183 )
15X-RAY DIFFRACTION15chain 'B' and (resid 184 through 218 )
16X-RAY DIFFRACTION16chain 'C' and (resid -1 through 26 )
17X-RAY DIFFRACTION17chain 'C' and (resid 27 through 54 )
18X-RAY DIFFRACTION18chain 'C' and (resid 55 through 73 )
19X-RAY DIFFRACTION19chain 'C' and (resid 74 through 112 )
20X-RAY DIFFRACTION20chain 'C' and (resid 113 through 131 )
21X-RAY DIFFRACTION21chain 'C' and (resid 132 through 160 )
22X-RAY DIFFRACTION22chain 'C' and (resid 161 through 183 )
23X-RAY DIFFRACTION23chain 'C' and (resid 184 through 217 )
24X-RAY DIFFRACTION24chain 'D' and (resid 0 through 26 )
25X-RAY DIFFRACTION25chain 'D' and (resid 27 through 89 )
26X-RAY DIFFRACTION26chain 'D' and (resid 90 through 112 )
27X-RAY DIFFRACTION27chain 'D' and (resid 113 through 160 )
28X-RAY DIFFRACTION28chain 'D' and (resid 161 through 183 )
29X-RAY DIFFRACTION29chain 'D' and (resid 184 through 203 )
30X-RAY DIFFRACTION30chain 'D' and (resid 204 through 217 )

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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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