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- PDB-5fjc: SAM-I riboswitch bearing the H. marismortui Kt-7 variant C-2bU -

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Basic information

Entry
Database: PDB / ID: 5fjc
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant C-2bU
ComponentsSAM-I RIBOSWITCH
KeywordsRNA / KINK TURN / RNA MOTIF / SAM-I RIBOSWITCH
Function / homology: / : / S-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
Biological speciesTHERMOANAEROBACTER TENGCONGENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsHuang, L. / Lilley, D.M.J.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function.
Authors: Huang, L. / Wang, J. / Lilley, D.M.J.
History
DepositionOct 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id / _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

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Assembly

Deposited unit
A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,27930
Polymers30,7681
Non-polymers3,51029
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.398, 60.398, 152.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-111-

BA

21A-121-

BA

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain SAM-I RIBOSWITCH


Mass: 30768.320 Da / Num. of mol.: 1 / Fragment: SAM BINDING DOMAIN / Source method: obtained synthetically
Source: (synth.) THERMOANAEROBACTER TENGCONGENSIS (bacteria)

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Non-polymers , 6 types, 212 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical...
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Ba
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMUTATION [A94G, C22U]

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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: 1.89 Å3/Da / Density % sol: 34.92 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 40 MM BACL2, 12 MM SPERMINE-HCL, 12% (V/V) MPD.

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2015 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.71→41.13 Å / Num. obs: 31465 / % possible obs: 99.7 % / Observed criterion σ(I): 1.2 / Redundancy: 9.6 % / Biso Wilson estimate: 32.74 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.2 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
ESRFAUTOPROCESSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B5R
Resolution: 1.71→41.134 Å / SU ML: 0.27 / σ(F): 1.33 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 2822 4.9 %
Rwork0.2009 --
obs0.2028 31391 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.4 Å2
Refinement stepCycle: LAST / Resolution: 1.71→41.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2037 55 183 2275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042390
X-RAY DIFFRACTIONf_angle_d1.1223733
X-RAY DIFFRACTIONf_dihedral_angle_d15.6281183
X-RAY DIFFRACTIONf_chiral_restr0.044489
X-RAY DIFFRACTIONf_plane_restr0.00899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7101-1.73960.40391330.37272536X-RAY DIFFRACTION92
1.7396-1.77120.34531380.34712817X-RAY DIFFRACTION100
1.7712-1.80530.30981340.31632763X-RAY DIFFRACTION100
1.8053-1.84210.32471400.30042770X-RAY DIFFRACTION100
1.8421-1.88220.31271280.28642808X-RAY DIFFRACTION100
1.8822-1.9260.31331790.27792748X-RAY DIFFRACTION100
1.926-1.97410.3141370.28652739X-RAY DIFFRACTION100
1.9741-2.02750.341330.27192818X-RAY DIFFRACTION100
2.0275-2.08710.31191270.26872803X-RAY DIFFRACTION100
2.0871-2.15450.31581420.24712768X-RAY DIFFRACTION100
2.1545-2.23150.28121140.24512787X-RAY DIFFRACTION100
2.2315-2.32090.31971490.23522806X-RAY DIFFRACTION100
2.3209-2.42650.31021420.22372757X-RAY DIFFRACTION100
2.4265-2.55440.26451730.21632743X-RAY DIFFRACTION100
2.5544-2.71440.24431540.21812758X-RAY DIFFRACTION100
2.7144-2.92390.25571450.21242784X-RAY DIFFRACTION100
2.9239-3.21810.23271550.17632763X-RAY DIFFRACTION100
3.2181-3.68350.20241650.16072748X-RAY DIFFRACTION100
3.6835-4.63980.16471120.14972827X-RAY DIFFRACTION100
4.6398-41.14590.21441220.18822749X-RAY DIFFRACTION99
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)
14.15351.3178-4.03896.5639-1.65454.0675-0.72781.76770.0445-0.70860.6281-0.33660.9399-0.06440.11660.4525-0.0717-0.00820.5866-0.0240.4335-0.667-13.90236.1422
24.9859-1.03931.59711.43970.07613.86550.06810.0041-0.1204-0.009-0.15310.3812-0.10060.04160.06690.3252-0.07070.04740.3204-0.04380.4553-16.0282-12.513134.3435
33.4892-4.4153.07175.941-3.10947.24990.13570.6618-0.6128-0.69760.33420.4560.9339-0.7107-0.58160.3066-0.0186-0.00830.5523-0.03030.474-23.5513-6.036220.114
40.13610.84110.2796.8518-0.96353.8033-0.18361.04171.3225-0.76840.59011.27380.5142-1.3166-0.46560.62460.1330.05031.31690.35110.6133-15.27459.57839.7289
53.2955-1.7124-1.33446.29724.03414.4710.39720.28930.6535-0.57530.0669-0.4437-0.59820.2099-0.47440.3255-0.05180.11950.42640.01190.43270.0297.38958.6937
63.5493.9473-1.65285.5126-0.42912.2157-0.10470.55740.25320.34820.29260.06730.24660.0244-0.11960.37340.0472-0.03150.41880.0210.3009-2.943-8.977113.726
75.53571.00163.2098.2081-0.54445.75370.26510.9215-0.359-0.6810.3527-1.31180.63381.1959-0.83820.33390.05620.0730.4882-0.10340.4252-3.3192-20.3613.3496
82.98642.8044-1.86042.7743-2.1842.00440.06720.2850.0305-0.4974-0.1201-0.0050.1732-0.2580.13290.3815-0.06240.00740.43720.03030.2597-6.7871-6.79343.7561
92.8745-1.8313-2.76656.0190.07483.16530.05280.17690.0782-0.13520.01110.23840.1044-0.8158-0.05520.18090.01360.02040.46510.04920.291-5.47513.18058.2105
106.46092.1816-4.3661.5773-2.15723.59430.37170.40720.97880.67010.30960.6421-0.6409-0.6131-0.72130.32180.09510.11560.44080.05240.5395-16.3638.319221.4615
112.1981-3.606-0.9579.6865-3.94028.3425-0.28920.12720.51630.83030.2923-0.0705-0.5806-0.9042-0.00150.3280.07330.08750.3707-0.04290.3721-18.31331.56836.3793
123.835-2.2321-1.70073.85892.27297.3102-0.2933-0.05040.02561.2750.36860.3657-0.1497-0.8587-0.04660.74310.11270.17150.40150.00730.4975-19.514911.273638.5249
134.8396-1.4466-1.0964.74960.95836.94680.34130.62980.5981-0.2945-0.021-0.58490.11580.4256-0.24020.29710.05620.08420.42350.02610.3758-12.4851.132824.7284
144.99350.4494-2.70086.5687-6.52469.35270.26640.2839-0.5398-0.20750.1920.87540.1876-1.071-0.51280.3716-0.1519-0.03180.5071-0.01150.3543-16.2994-10.679715.2367
150.89771.5341-0.81132.6115-1.87253.6672-0.0842-0.0372-0.2667-0.07570.0412-0.0275-0.06690.36890.07360.2732-0.03790.04070.4293-0.03540.3361-11.0565-22.437217.8727
165.47415.742-0.07368.58112.6185.13070.4133-0.6115-0.30420.0528-0.4216-0.1280.2345-0.0363-0.10080.32140.0492-0.010.36330.04010.3034-19.1337-35.793323.1547
177.9904-2.7017-5.20974.6573.58958.7244-0.13260.0808-0.17460.41410.1951-0.13650.48420.71460.01510.33970.0481-0.00850.38920.02220.2882-19.7359-35.916512.3351
188.89195.45332.66336.83933.69842.2030.3079-0.47840.55720.3601-0.2121-0.0822-0.37260.4127-0.07290.3617-0.07110.03110.4074-0.01270.3567-16.8086-24.947426.9198
190.9378-1.0175-0.14076.44593.06714.3997-0.0582-0.04830.23340.37620.0803-0.31220.10970.20720.05020.2422-0.0246-0.02210.3099-0.02540.298-8.8525-10.005930.6032
205.9321-3.11591.80566.7948-1.09715.0678-0.2116-0.14341.0616-0.10030.1162-0.294-0.17890.40250.09980.3942-0.0909-0.0170.35060.00310.44230.2667-7.685242.2619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:8)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 9:12)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 13:16)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 17:20)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 21:24)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 25:28)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 29:33)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 34:39)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 40:45)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 46:49)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 50:56)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 57:60)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 61:64)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 65:69)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 70:73)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 74:80)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 81:84)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 85:90)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 91:94)

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