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- PDB-4xk4: E. coli transcriptional regulator RUTR with dihydrouracil -

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Basic information

Entry
Database: PDB / ID: 4xk4
TitleE. coli transcriptional regulator RUTR with dihydrouracil
ComponentsHTH-type transcriptional regulator RutR
KeywordsTranscription Regulator / STRUCTURAL GENOMICS / PSI-BIOLOGY / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / HELIX-TURN-HELIX / TRANSCRIPTIONAL REGULATOR
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
Transcription regulator YcdC, C-terminal / Transcription regulator, pyrimidine utilisation, RutR / YcdC-like protein, C-terminal region / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like ...Transcription regulator YcdC, C-terminal / Transcription regulator, pyrimidine utilisation, RutR / YcdC-like protein, C-terminal region / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / HTH-type transcriptional regulator RutR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsShumilin, I.A. / Cooper, D.R. / Shabalin, I.G. / Grabowski, M. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-5U54GM094662 United States
CitationJournal: to be published
Title: E. COLI TRANSCRIPTIONAL REGULATOR RUTR WITH DIHYDROURACIL
Authors: Minor, W.
History
DepositionJan 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator RutR
B: HTH-type transcriptional regulator RutR
C: HTH-type transcriptional regulator RutR
D: HTH-type transcriptional regulator RutR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3238
Polymers94,8664
Non-polymers4564
Water4,288238
1
A: HTH-type transcriptional regulator RutR
B: HTH-type transcriptional regulator RutR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6614
Polymers47,4332
Non-polymers2282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-37 kcal/mol
Surface area16720 Å2
MethodPISA
2
C: HTH-type transcriptional regulator RutR
D: HTH-type transcriptional regulator RutR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6614
Polymers47,4332
Non-polymers2282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-40 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.892, 55.672, 85.242
Angle α, β, γ (deg.)88.37, 88.80, 62.37
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA17 - 21217 - 212
21ARGARGBB17 - 21217 - 212
12PROPROAA17 - 21117 - 211
22PROPROCC17 - 21117 - 211
13ARGARGAA17 - 21217 - 212
23ARGARGDD17 - 21217 - 212
14PROPROBB17 - 21117 - 211
24PROPROCC17 - 21117 - 211
15ARGARGBB17 - 21217 - 212
25ARGARGDD17 - 21217 - 212
16PROPROCC17 - 21117 - 211
26PROPRODD17 - 21117 - 211

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
HTH-type transcriptional regulator RutR / Rut operon repressor


Mass: 23716.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rutR, ycdC, b1013, JW0998 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P0ACU2
#2: Chemical
ChemComp-DUC / DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / DIHYDROURACIL


Mass: 114.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 nl of 10 mg/ml protein in 10 mM HEPES pH 7.5, 500 mM NaCl, 5 mM dihydrouracil was mixed with 200 nl 50 mM Ammonium Slufate, 50 mM BIS-TRIS, pH 6.5, 30% (v/v) Pentaerythirtol ethoxylate ...Details: 200 nl of 10 mg/ml protein in 10 mM HEPES pH 7.5, 500 mM NaCl, 5 mM dihydrouracil was mixed with 200 nl 50 mM Ammonium Slufate, 50 mM BIS-TRIS, pH 6.5, 30% (v/v) Pentaerythirtol ethoxylate and suspended over a reservoir of 1.5M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.27→50.01 Å / Num. all: 81777 / Num. obs: 37742 / % possible obs: 97.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.6
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.67 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JYK
Resolution: 2.27→50.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 19.489 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22539 1827 4.9 %RANDOM
Rwork0.19407 ---
obs0.19566 35540 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.064 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å2-2.29 Å2-1.92 Å2
2---1.39 Å20.74 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.27→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6133 0 32 238 6403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196301
X-RAY DIFFRACTIONr_bond_other_d0.0070.026168
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9648550
X-RAY DIFFRACTIONr_angle_other_deg1.3512.9914140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9895783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70623.672256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.122151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2761535
X-RAY DIFFRACTIONr_chiral_restr0.0780.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0227026
X-RAY DIFFRACTIONr_gen_planes_other0.0120.0221425
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_it1.3263.6553144
X-RAY DIFFRACTIONr_mcbond_other1.3263.6553143
X-RAY DIFFRACTIONr_mcangle_it2.0935.4783923
X-RAY DIFFRACTIONr_mcangle_other2.0935.4783924
X-RAY DIFFRACTIONr_scbond_it1.5583.8073157
X-RAY DIFFRACTIONr_scbond_other1.5583.8073158
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5785.6414627
X-RAY DIFFRACTIONr_long_range_B_refined4.0329.1817209
X-RAY DIFFRACTIONr_long_range_B_other3.97529.0697161
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A235780.09
12B235780.09
21A233820.07
22C233820.07
31A232840.08
32D232840.08
41B231240.07
42C231240.07
51B236920.04
52D236920.04
61C230440.07
62D230440.07
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 95 -
Rwork0.298 2533 -
obs--92.11 %
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)
12.70740.9164-1.10973.3724.46049.7017-0.1869-0.1394-0.0957-0.14280.3876-0.1179-0.17710.6657-0.20070.0724-0.06260.01820.1682-0.00370.0126-6.09-15.6245.371
20.24310.7251-1.06332.1679-3.17664.6567-0.0071-0.0274-0.0172-0.045-0.0739-0.05760.04860.1250.0810.1464-0.130.03350.2024-0.01890.0095-11.718-16.326.808
31.24871.5060.33244.60570.9140.70590.0831-0.17560.14530.4404-0.02560.22310.0224-0.0676-0.05750.1275-0.07430.0180.15840.00640.04011.6195.4211.936
41.90192.36370.09643.2303-0.51481.7264-0.1551-0.12370.393-0.1791-0.03560.4574-0.184-0.38260.19070.10250.0093-0.11150.2143-0.00370.1576-4.2079.247-8.056
53.3262-0.57310.72782.91120.25612.03360.0205-0.13880.09440.0991-0.0038-0.15370.01890.1538-0.01660.0638-0.0854-0.0350.15560.04020.025512.926-0.312-2.561
60.46010.28790.274210.8395-2.20671.7429-0.139-0.06190.0194-0.05470.1669-0.2444-0.24910.0494-0.02790.117-0.0473-0.02590.13030.01170.068614.06415.714-5.29
71.7505-0.44870.38894.1535-0.16858.1986-0.24220.1751-0.19710.00130.02230.00330.27470.07290.21990.1251-0.1020.05260.1132-0.01970.04613.505-22.377-24.945
81.09331.6869-0.00895.93961.36410.5905-0.16660.1318-0.1068-0.21060.2053-0.31820.04810.0245-0.03870.1804-0.09860.03810.14570.01730.041215.255-7.97-23.032
92.2937-0.77272.92444.0684-1.38835.1943-0.0631-0.0109-0.0881-0.31030.11490.02470.3253-0.3032-0.05180.2047-0.13130.0150.17090.02850.02586.465-9.095-17.051
1010.53675.2358-0.2842.9221-0.28082.47850.53770.3721-0.18660.2813-0.0573-0.29310.4730.1038-0.48050.2805-0.0349-0.07110.21720.1150.296121.057-11.634-12.968
113.14151.2120.11112.16040.4071.2665-0.06570.0738-0.1264-0.32190.0807-0.1014-0.1340.0605-0.01510.1284-0.0837-0.02150.13410.03320.022812.2415.062-15.376
1210.56737.75151.47.53073.6063.8045-0.0696-0.04170.3894-0.29410.02020.2647-0.32740.0860.04930.1903-0.0625-0.01460.1010.08090.092113.57715.17-15.688
132.46611.47123.16113.02442.36154.3078-0.0271-0.07680.1507-0.0241-0.16330.0584-0.0772-0.16270.19040.1191-0.1161-0.02090.21310.030.0164-5.004-9.17-36.64
141.85260.67590.430912.40161.87330.44710.1981-0.2458-0.21030.4052-0.0411-0.41660.1413-0.0239-0.15710.1023-0.0791-0.0880.12750.04970.0841-9.89-31.092-39.314
153.0575-0.72121.025611.55341.88461.54020.3179-0.5742-0.19260.84750.1055-0.00970.3953-0.1066-0.42350.2465-0.1612-0.1110.25280.0440.1795-20.335-34.421-38.35
162.33191.4231.27591.59340.81012.86440.2471-0.2032-0.57590.04130.0424-0.43790.09660.19-0.28950.0662-0.0991-0.0450.2370.04480.1609-8.552-28.053-47.856
171.41181.86460.57412.8511-0.05041.96150.2885-0.1764-0.10320.3085-0.0895-0.05230.2749-0.2815-0.1990.1648-0.1189-0.0280.30590.0740.0328-23.737-30.828-46.717
184.9118-0.25140.91569.52146.4024.60020.2485-0.6571-0.50720.58-0.13740.11140.4822-0.2565-0.11120.2219-0.148-0.04790.19330.09920.1527-27.737-40.326-44.718
195.44370.7736-0.50336.7802-0.6743.8014-0.1299-0.02080.3079-0.15250.02610.0311-0.10110.19390.10370.0836-0.0667-0.04920.08840.01940.0514-20.395-5.4-67.17
206.47950.23351.61087.19840.24750.4896-0.34880.19560.27020.13920.26890.4999-0.14790.00070.07990.1544-0.0384-0.03760.16980.03310.0695-25.971-3.524-67.96
213.62592.46030.93219.086-0.49061.6520.02880.04090.0763-0.5810.06750.26420.1858-0.3635-0.09630.1195-0.1037-0.03860.19670.04550.0173-33.588-31.296-63.373
222.54890.0046-0.962.98350.50024.21440.04520.04520.2204-0.22760.0397-0.0509-0.1605-0.2308-0.08490.0459-0.06020.00190.18050.01770.0213-23.562-18.452-59.075
232.23421.5853-0.82084.1641-1.60451.12980.1547-0.19190.1945-0.0973-0.05980.71850.1545-0.3659-0.0950.0994-0.2072-0.02420.5082-0.0490.2551-39.723-30.43-54.369
242.91981.409-0.13721.9873-0.38271.84690.1794-0.0391-0.2484-0.0811-0.015-0.30170.3419-0.2079-0.16440.151-0.0988-0.02980.21170.0180.0746-20.903-33.936-57.293
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 42
2X-RAY DIFFRACTION2A43 - 69
3X-RAY DIFFRACTION3A70 - 116
4X-RAY DIFFRACTION4A117 - 162
5X-RAY DIFFRACTION5A163 - 198
6X-RAY DIFFRACTION6A199 - 212
7X-RAY DIFFRACTION7B17 - 50
8X-RAY DIFFRACTION8B51 - 102
9X-RAY DIFFRACTION9B103 - 125
10X-RAY DIFFRACTION10B126 - 137
11X-RAY DIFFRACTION11B138 - 197
12X-RAY DIFFRACTION12B198 - 212
13X-RAY DIFFRACTION13C17 - 69
14X-RAY DIFFRACTION14C70 - 87
15X-RAY DIFFRACTION15C88 - 109
16X-RAY DIFFRACTION16C110 - 149
17X-RAY DIFFRACTION17C150 - 194
18X-RAY DIFFRACTION18C195 - 212
19X-RAY DIFFRACTION19D17 - 45
20X-RAY DIFFRACTION20D46 - 72
21X-RAY DIFFRACTION21D73 - 99
22X-RAY DIFFRACTION22D100 - 129
23X-RAY DIFFRACTION23D130 - 159
24X-RAY DIFFRACTION24D160 - 212

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