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- PDB-2qbz: Structure of the M-Box Riboswitch Aptamer Domain -

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Basic information

Entry
Database: PDB / ID: 2qbz
TitleStructure of the M-Box Riboswitch Aptamer Domain
ComponentsM-Box RNA, ykoK riboswitch aptamer
KeywordsRNA / riboswitch / ykoK / M-Box / RNA sensor / Noncoding RNA
Function / homology: / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.6 Å
AuthorsDann III, C.E. / Winkler, W.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structure and mechanism of a metal-sensing regulatory RNA
Authors: Dann III, C.E. / Wakeman, C.A. / Sieling, C.L. / Baker, S.C. / Irnov, I. / Winkler, W.C.
History
DepositionJun 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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_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_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.value / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: M-Box RNA, ykoK riboswitch aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,11311
Polymers51,8111
Non-polymers30210
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.655, 101.081, 285.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: RNA chain M-Box RNA, ykoK riboswitch aptamer


Mass: 51810.707 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence naturally appears in Bacillus subtilis. It was produced by T7 RNA pol in vitro transcription.
References: GenBank: 32468738
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews3/Da)Density % sol (%)
13.3963.72
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop7.4HEPES, MPD, Spermine, KCl, MgCl2 over 35 % MPD, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop7.2HEPES, MPD, Spermine, CsCl, MgCl2 over 35 % MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2MPD11
3MPD12
4Spermine11
5KCl11
6MgCl211
7HEPES21
8MPD21
9MPD22
10Spermine21
11CsCl21
12MgCl221

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9786
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDApr 17, 2006
RIGAKU RAXIS IV2IMAGE PLATEJun 17, 2006osmic mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SILICON 111SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
21.54181
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
4.216.21052030.1070.922.52517498.6
3.1210391370.1111.222.91253276.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385097.710.0660.7544
4.275.3899.810.0830.8734.1
3.734.2799.710.0850.9234.2
3.393.7399.810.1010.954.2
3.153.3999.610.1150.9684.3
2.963.1599.510.1540.9644.3
2.822.9699.410.2540.9134.3
2.692.8299.210.3720.9254.3
2.592.6998.510.4140.9384.2
2.52.5992.710.5730.9854
6.245067.320.0651.7183.5
4.966.2473.120.0721.5763.4
4.334.9674.820.0841.1583.4
3.944.3376.820.1031.1363.3
3.653.9477.720.1241.1483.3
3.443.6578.520.1511.043.1
3.273.4480.320.1741.0733
3.123.2779.320.211.1062.9
33.128020.3111.0342.8
2.9380.520.4591.0092.6
ReflectionResolution: 2.6→50 Å / Num. all: 22584 / Num. obs: 22584 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Χ2: 1.006 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3 / Num. unique all: 2202 / Rsym value: 0.401 / Χ2: 1.046 / % possible all: 98.7

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Phasing

PhasingMethod: SIRAS
Phasing set
ID
1
2
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 24487
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.25-100610.792508
7.31-9.2563.50.832510
6.35-7.3159.20.821519
5.75-6.3558.90.863531
5.29-5.7555.30.874568
4.93-5.2961.80.872610
4.63-4.9359.90.856663
4.38-4.6361.20.871680
4.17-4.3865.90.882754
3.99-4.1762.60.897759
3.82-3.9964.60.904804
3.68-3.8266.10.896833
3.55-3.6866.40.899877
3.44-3.55710.893888
3.33-3.44680.903934
3.23-3.3370.80.887942
3.15-3.2368.70.8961007
3.06-3.1572.60.88979
2.99-3.0676.20.8671042
2.92-2.9979.10.8341066
2.85-2.9288.70.821060
2.79-2.8589.20.7891117
2.73-2.7990.30.7941113
2.68-2.7390.10.7781146
2.63-2.6890.50.7921184
2.58-2.63910.7991186
2.5-2.5888.70.6972207
Phasing MIR der

Native set-ID: 1 / Resolution: 2.5→37.85 Å

IDDer set-IDPower acentricPower centricReflection acentricReflection centric
ISO_1100219212566
ISO_221.4881.228104501260
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDPower acentricPower centricReflection acentricReflection centric
10.7437.85ISO_100217113
7.7510.74ISO_100407120
6.387.75ISO_100539115
5.546.38ISO_100652131
4.975.54ISO_100762122
4.544.97ISO_100838124
4.214.54ISO_100926131
3.944.21ISO_1001000126
3.723.94ISO_1001064126
3.533.72ISO_1001146128
3.373.53ISO_1001199135
3.223.37ISO_1001260130
3.13.22ISO_1001322136
2.993.1ISO_1001356133
2.882.99ISO_1001415135
2.792.88ISO_1001473136
2.712.79ISO_1001517130
2.632.71ISO_1001571141
2.562.63ISO_1001597130
2.52.56ISO_1001660124
10.7437.85ISO_22.1931.40715074
7.7510.74ISO_22.4061.60228681
6.387.75ISO_22.2791.84639679
5.546.38ISO_22.0991.45547687
4.975.54ISO_21.9561.8655786
4.544.97ISO_21.7641.55261686
4.214.54ISO_21.7011.2668490
3.944.21ISO_21.5921.11375883
3.723.94ISO_21.4831.09579487
3.533.72ISO_21.3360.98386991
3.373.53ISO_21.1930.80691586
3.223.37ISO_21.0840.75295388
3.13.22ISO_21.0490.702100387
2.993.1ISO_20.9350.636101283
2.882.99ISO_20.8290.52598172
2.792.88ISO_20000
2.712.79ISO_20000
2.632.71ISO_20000
2.562.63ISO_20000
2.52.56ISO_20000

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM6phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.6→47.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.412 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.363 / ESU R Free: 0.263 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1131 5.1 %RANDOM
Rwork0.202 ---
all0.204 22181 --
obs0.204 22181 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.551 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å20 Å2
2---1.64 Å20 Å2
3---5.47 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3263 10 135 3408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213683
X-RAY DIFFRACTIONr_angle_refined_deg1.7335683
X-RAY DIFFRACTIONr_chiral_restr0.080.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021579
X-RAY DIFFRACTIONr_nbd_refined0.1990.21543
X-RAY DIFFRACTIONr_nbtor_refined0.2790.22296
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2204
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.27
X-RAY DIFFRACTIONr_mcbond_it1.81.523
X-RAY DIFFRACTIONr_scbond_it1.12633849
X-RAY DIFFRACTIONr_scangle_it1.6034.55683
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 79 -
Rwork0.323 1515 -
obs-1594 99.13 %
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)
15.350.38294.08371.10821.44734.35140.1859-0.3331-0.7790.2156-0.03960.04550.0117-0.1047-0.14630.0682-0.048-0.0182-0.01940.07550.33213.1910.87269.482
23.45150.1361.52591.62320.47751.47370.0956-0.32760.7073-0.0530.0314-0.171-0.0953-0.2174-0.1270.00660.01530.0463-0.0064-0.07530.195129.26531.93890.431
39.2466-2.76680.6366.6257-1.83313.5046-1.3365-1.49870.54441.54170.871-0.8318-1.1015-1.78650.46540.27880.3759-0.23230.5055-0.5426-0.036534.77139.904120.377
42.6280.11871.29120.99140.8171.66220.0966-0.36320.00830.00270.0519-0.21140.21230.0557-0.1485-0.00930.0263-0.01260.0753-0.02130.172541.45815.61896.804
52.3007-0.24050.37370.2438-0.00230.840.0829-0.7297-0.0285-0.00690.0159-0.06460.0774-0.1872-0.09890.0123-0.0179-0.0080.1880.01140.103629.69118.54999.166
63.84370.18962.28631.0709-0.10726.5637-0.6183-1.57261.07611.03360.2146-0.2889-0.857-1.17860.40370.19580.3133-0.27470.7562-0.60550.016639.38737.127121.263
73.4130.37120.23761.9651-0.27840.07050.1197-0.21590.3967-0.0135-0.0808-0.10030.109-0.1969-0.0389-0.01930.0040.0442-0.0475-0.00950.233528.52530.09384.555
82.6381-1.49381.28320.8637-0.55812.21130.1493-0.1457-0.3444-0.08180.17370.35360.3667-0.1195-0.32290.0742-0.042-0.0624-0.09240.04740.376511.4188.92970.085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA15 - 241 - 10
2X-RAY DIFFRACTION2XA25 - 3611 - 22
3X-RAY DIFFRACTION3XA37 - 4923 - 35
4X-RAY DIFFRACTION4XA50 - 7536 - 61
5X-RAY DIFFRACTION5XA76 - 11862 - 104
6X-RAY DIFFRACTION6XA119 - 148105 - 134
7X-RAY DIFFRACTION7XA149 - 162135 - 148
8X-RAY DIFFRACTION8XA163 - 175149 - 161

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