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- PDB-3qoc: Crystal structure of N-terminal domain (Creatinase/Prolidase like... -

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Basic information

Entry
Database: PDB / ID: 3qoc
TitleCrystal structure of N-terminal domain (Creatinase/Prolidase like domain) of putative metallopeptidase from Corynebacterium diphtheriae
ComponentsPutative metallopeptidase
KeywordsHYDROLASE / MCSG / PSI-2 / Structural Genomics / Midwest Center for Structural Genomics
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 ...Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative metallopeptidase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsNocek, B. / Stein, A. / Marshall, N. / Putagunta, R. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of N-terminal domain (Creatinase/Prolidase like domain) of putative metallopeptidase from Corynebacterium diphtheriae
Authors: Nocek, B. / Stein, A. / Marshall, N. / Putagunta, R. / Feldmann, B. / Joachimiak, A.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative metallopeptidase
B: Putative metallopeptidase
C: Putative metallopeptidase
D: Putative metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,86210
Polymers59,4074
Non-polymers4556
Water2,108117
1
A: Putative metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9833
Polymers14,8521
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0443
Polymers14,8521
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8872
Polymers14,8521
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9482
Polymers14,8521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.013, 82.588, 104.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Putative metallopeptidase


Mass: 14851.664 Da / Num. of mol.: 4 / Fragment: sequence database residues 4-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DIP1341 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q6NH06
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium acetate 0.1 M HEPES 7.5 45% 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 37532 / Num. obs: 37532 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 27
Reflection shellResolution: 2.15→2.23 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXmodel building
ARP/wARPmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 10.567 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.202 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25392 1867 5 %RANDOM
Rwork0.20742 ---
all0.21 37356 --
obs0.2098 35489 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2--1.75 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 22 117 3907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223843
X-RAY DIFFRACTIONr_bond_other_d0.0010.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.985220
X-RAY DIFFRACTIONr_angle_other_deg1.02836221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78623.067150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25415639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0591536
X-RAY DIFFRACTIONr_chiral_restr0.1110.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02755
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_it1.0531.52529
X-RAY DIFFRACTIONr_mcbond_other0.2951.51023
X-RAY DIFFRACTIONr_mcangle_it1.89324039
X-RAY DIFFRACTIONr_scbond_it3.13731314
X-RAY DIFFRACTIONr_scangle_it4.8344.51179
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.148→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 110 -
Rwork0.258 2276 -
obs--86.67 %
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)
14.904-1.72324.26890.8187-1.11973.5239-0.0501-0.4142-0.03010.11330.1867-0.2095-0.0069-0.3918-0.13660.185-0.0392-0.02830.235-0.04680.129124.704828.562634.3923
25.79582.5502-0.43534.63533.58933.48870.1868-0.50850.07790.3196-0.17980.02180.21880.0331-0.0070.1799-0.00230.01130.205-0.00560.063416.202428.770629.7463
34.4754-5.3116-0.23857.16643.72478.14730.054-0.0165-0.04540.0249-0.24690.17230.1558-0.59310.19290.0777-0.05970.10430.2374-0.02110.2235.648324.163925.4596
41.4899-0.2132-0.24991.0590.20980.80740.0325-0.0465-0.01910.0192-0.01960.0041-0.0010.0043-0.01290.1170.00320.00720.1355-0.00140.092419.978225.649117.9536
51.7171-1.5963-2.84892.52950.23657.0881-0.013-0.13280.1057-0.0217-0.0056-0.2390.11230.32960.01860.108-0.0164-0.0110.1819-0.03310.16430.951823.968119.4679
62.03220.73481.30312.44141.02183.67160.04510.0567-0.1404-0.03030.0141-0.02840.09490.0555-0.05920.12280.00740.00120.1158-0.00340.139621.63617.91513.9849
716.64842.4471-7.53087.69411.50994.06540.0697-0.5961-0.6280.392-0.177-0.48930.10960.24330.10720.171-0.0053-0.10720.24470.04550.141610.196111.796717.6535
80.371-0.45231.10861.8205-1.41862.666-0.0332-0.07820.02720.00240.0025-0.0001-0.0562-0.16950.03070.1011-0.00630.00910.16520.00730.16056.868526.695812.3082
93.08145.5199-1.871519.6445-6.54112.9968-0.05620.11340.1174-0.39090.2057-0.01130.204-0.2775-0.14950.1-0.0155-0.02410.19180.00460.12437.431617.70217.2856
102.95641.32330.20653.5635-1.05630.77660.1833-0.11450.26780.0989-0.20050.5635-0.0115-0.14760.01710.1125-0.00090.0160.2105-0.03340.19644.244123.36216.9563
110.0753-0.66460.60343.6582-3.9093.50590.07930.04970.0341-0.2343-0.0560.0550.23560.082-0.02330.1718-0.020.01440.23010.05430.12138.3647.5274-22.7898
121.49654.46321.03810.54642.62921.5716-0.23190.12190.0124-0.54310.22690.05570.0711-0.0120.0050.18810.0395-0.00110.2641-0.02130.08225.847638.2418-17.8163
139.9405-3.7105-2.98254.8189-1.77314.18990.0223-0.015-0.1703-0.4088-0.04060.07550.08270.20460.01820.1343-0.0375-0.01330.1826-0.04520.1410.423628.9107-13.7879
144.91021.4138-0.4752.264-0.70010.7507-0.1311-0.0861-0.0306-0.03310.0825-0.0401-0.03980.00980.04870.11790.00070.00680.14540.00520.11657.756240.014-5.3429
153.45560.353-1.11680.10320.3291.5864-0.0004-0.020.1092-0.01710.02790.037-0.10960.1054-0.02750.16620.00290.00780.1339-0.00520.1227.987946.3418-5.9987
161.89760.7019-0.40743.61011.62342.8631-0.01650.0135-0.0416-0.0181-0.06750.22730.0626-0.23270.08410.09660.031-0.00430.12340.02910.1312-1.16543.7993-8.9224
171.3258-0.45060.41074.6661.392815.3899-0.01650.09230.49180.03020.0980.1634-0.5026-0.0581-0.08150.120.00860.02370.12740.03240.20644.321655.2426-7.0877
181.47180.86650.42011.1033-0.71822.82130.1071-0.09150.22410.1547-0.05470.1542-0.1699-0.0859-0.05230.10210.01750.01690.16120.00040.1366-3.241546.2444-2.1398
194.57470.97750.42121.37790.43360.9677-0.01110.070.0737-0.06810.01640.1347-0.0286-0.1046-0.00530.1352-0.0043-0.00250.13290.02060.1263-6.518933.7754-6.7
202.1853-0.25671.0570.6380.41711.19220.0901-0.1029-0.0244-0.00070.0185-0.01610.0095-0.13-0.10860.114-0.01380.01190.14710.03340.1533-1.628431.02460.5087
217.9519-8.30652.7168-3.90332.05965.59460.55350.3946-1.31620.112-0.04090.65711.95491.8586-0.51260.63860.3114-0.2420.79510.12710.391647.154529.88823.6346
225.8228-1.28650.03710.457-0.72620.5346-0.3238-0.31560.540.19510.2273-0.621-0.00810.26670.09640.0742-0.0284-0.04220.2115-0.01020.222743.929838.5576-2.5028
236.7233-2.09081.04162.47840.36660.147-0.21530.5871.052-0.01950.0331-0.37860.00650.13230.18220.1443-0.05020.00730.18440.1110.397135.464148.1331-7.175
243.1287-0.2593-0.23651.4351-1.02772.0734-0.04270.0761-0.0115-0.08360.02-0.04790.1625-0.02610.02270.12210.0010.00980.13890.00620.101335.477430.7497-7.4668
251.9721-0.0833-0.11165.8827-1.32371.5044-0.1254-0.06190.08030.16750.018-0.0872-0.04460.00390.10740.10680.01170.00360.16720.01370.086331.678432.33220.3489
262.1423-1.01620.27291.9416-0.8671.8945-0.099-0.0529-0.0380.01730.0459-0.0004-0.03120.0110.05310.09770.00090.01630.14550.00260.109629.836529.9650.5911
278.1009-4.3092-0.28555.427-6.43979.569-0.2564-0.98950.42030.7160.1432-0.3925-0.90280.49530.11320.1874-0.0087-0.00430.2153-0.04320.230923.197245.76110.4828
282.65310.12610.79020.84512.22554.7677-0.02350.09280.1222-0.04510.0394-0.0322-0.07470.1421-0.01590.15330.01460.0160.13090.07450.144629.578140.1454-14.0789
296.5401-2.0478-11.77399.11413.97722.0199-0.0789-0.146-0.2072-0.10910.02650.01190.3318-0.31310.05240.1064-0.0258-0.00070.16210.0540.13220.183435.0417-15.1098
305.98010.6343-1.46331.7003-0.47092.3452-0.0843-0.19280.3188-0.2405-0.0879-0.04730.05980.150.17220.11470.01760.00660.12240.04690.158425.096743.3507-10.7052
314.688-3.90583.7648.58751.25326.2169-0.39150.43410.7606-0.0006-0.1085-0.8108-0.69280.68570.50.2022-0.2015-0.06750.14480.10020.37422.630262.655416.7145
323.5619-1.3063-1.39754.24590.41332.5171-0.2995-0.52010.25370.4340.0901-0.1592-0.4880.00180.20940.27450.0359-0.1080.1591-0.08370.158812.984758.799121.8269
337.7811-0.2253-5.74271.3631-0.14023.32040.1351-0.33190.20150.2757-0.0694-0.1146-0.23050.0778-0.06570.26730.0901-0.11970.2432-0.04420.16746.73659.586217.1999
341.6351-0.12682.33712.83890.1582.7159-0.28290.21730.2396-0.1649-0.0708-0.2509-0.35390.25040.35360.212-0.04170.00390.12380.04550.183415.217554.506112.5405
357.3421-1.3723.52084.8134-0.70975.9195-0.03160.349-0.0429-0.0963-0.02020.1992-0.4059-0.35240.05180.21610.0483-0.00060.074-0.02160.13492.505457.997510.6895
363.0165-1.72671.8323.8905-2.44874.194-0.05290.2445-0.0365-0.0183-0.13380.0115-0.18340.0910.18670.1453-0.01130.00430.1299-0.01370.109610.873750.763911.6359
3716.6581-0.640511.6391.96712.491111.48770.23841.23870.5274-0.5818-0.2092-0.2727-0.6350.7083-0.02920.2001-0.04670.09530.27960.07780.223423.056844.324311.5321
380.47770.6498-1.00793.09450.61893.35030.0589-0.03540.0717-0.0091-0.07640.081-0.2758-0.02550.01760.14370.0305-0.08190.1413-0.00530.191617.568949.580226.7699
395.1432-1.8058-2.36023.8403-0.17143.8660.0429-0.10240.06530.001-0.1331-0.357-0.08880.22390.09020.1267-0.0069-0.0060.1457-0.0220.150219.748940.667521.1335
4014.0282-6.0015-1.54840.5052.80967.56260.0418-0.12751.15790.16970.1037-1.0632-0.1171-0.1492-0.14560.2409-0.0367-0.48010.2228-0.05680.917722.33553.749526.5672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 11
2X-RAY DIFFRACTION2A12 - 17
3X-RAY DIFFRACTION3A18 - 29
4X-RAY DIFFRACTION4A30 - 66
5X-RAY DIFFRACTION5A67 - 75
6X-RAY DIFFRACTION6A76 - 89
7X-RAY DIFFRACTION7A90 - 97
8X-RAY DIFFRACTION8A98 - 109
9X-RAY DIFFRACTION9A110 - 120
10X-RAY DIFFRACTION10A121 - 131
11X-RAY DIFFRACTION11B3 - 12
12X-RAY DIFFRACTION12B13 - 19
13X-RAY DIFFRACTION13B20 - 28
14X-RAY DIFFRACTION14B29 - 38
15X-RAY DIFFRACTION15B39 - 49
16X-RAY DIFFRACTION16B50 - 65
17X-RAY DIFFRACTION17B66 - 75
18X-RAY DIFFRACTION18B76 - 90
19X-RAY DIFFRACTION19B91 - 102
20X-RAY DIFFRACTION20B103 - 128
21X-RAY DIFFRACTION21C4 - 9
22X-RAY DIFFRACTION22C10 - 18
23X-RAY DIFFRACTION23C19 - 29
24X-RAY DIFFRACTION24C30 - 51
25X-RAY DIFFRACTION25C52 - 68
26X-RAY DIFFRACTION26C69 - 91
27X-RAY DIFFRACTION27C92 - 97
28X-RAY DIFFRACTION28C98 - 107
29X-RAY DIFFRACTION29C108 - 113
30X-RAY DIFFRACTION30C114 - 131
31X-RAY DIFFRACTION31D8 - 28
32X-RAY DIFFRACTION32D29 - 39
33X-RAY DIFFRACTION33D40 - 47
34X-RAY DIFFRACTION34D48 - 64
35X-RAY DIFFRACTION35D65 - 74
36X-RAY DIFFRACTION36D75 - 90
37X-RAY DIFFRACTION37D91 - 97
38X-RAY DIFFRACTION38D98 - 110
39X-RAY DIFFRACTION39D111 - 123
40X-RAY DIFFRACTION40D124 - 131

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  • Now, EM Navigator and Yorodumi are based on the updated data.

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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