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- PDB-4jrc: Distal Stem I region from G. kaustophilus glyQS T box RNA -

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Basic information

Entry
Database: PDB / ID: 4jrc
TitleDistal Stem I region from G. kaustophilus glyQS T box RNA
ComponentsDistal Stem I region of the glyQS T box leader RNA
KeywordsRNA / T box RNA / Regulatory RNA leader sequence / tRNA binding
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.673 Å
AuthorsGrigg, J.C. / Ke, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: T box RNA decodes both the information content and geometry of tRNA to affect gene expression.
Authors: Grigg, J.C. / Chen, Y. / Grundy, F.J. / Henkin, T.M. / Pollack, L. / Ke, A.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Feb 28, 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
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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Distal Stem I region of the glyQS T box leader RNA
B: Distal Stem I region of the glyQS T box leader RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3594
Polymers37,3102
Non-polymers492
Water45025
1
A: Distal Stem I region of the glyQS T box leader RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6792
Polymers18,6551
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Distal Stem I region of the glyQS T box leader RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6792
Polymers18,6551
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.461, 41.511, 90.417
Angle α, β, γ (deg.)90.000, 106.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain Distal Stem I region of the glyQS T box leader RNA


Mass: 18655.002 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthesized in vitro using T7 RNA polymerase from a plasmid template
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 80mM NaCl, 12mM KCl, 20mM MgCl2, 40mM sodium cacodylate, 12mM spermine, 28% 2-methyl-1,3 propanediol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2012
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionRedundancy: 9.5 % / Number: 52864 / Rmerge(I) obs: 0.231 / Χ2: 3.58 / D res high: 3.5 Å / D res low: 35 Å / Num. obs: 5591 / % possible obs: 94.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
9.443599.110.13221.1626.9
7.529.4410010.1359.9958.9
6.577.5299.710.1455.70710.1
5.986.5710010.1874.01911.4
5.555.9810010.2113.73711.5
5.225.5510010.2693.25111.8
4.965.2210010.3062.63212
4.754.9610010.3422.09712.1
4.574.7510010.3731.91211.7
4.414.5710010.3691.84911.4
4.274.4110010.4231.62710.6
4.154.2799.710.4131.6679.9
4.044.159910.2391.7269.1
3.944.0496.410.3491.798.4
3.853.9495.410.4781.597.7
3.773.8589.910.4591.2867.1
3.693.7785.310.3941.3817
3.623.6981.210.4441.3276.7
3.563.6275.110.5411.2646.1
3.53.5672.210.4971.1815.7
ReflectionResolution: 2.65→35 Å / Num. obs: 11578 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 48.89 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.65-2.73.10.4841.808473182.7
2.7-2.743.10.4821.931529185.6
2.74-2.83.30.4182.041508190.1
2.8-2.853.40.3233.086534194.2
2.85-2.923.40.3053.507615197.5
2.92-2.983.60.2185.286571199.1
2.98-3.063.60.2125.9425721100
3.06-3.143.60.149.8225881100
3.14-3.233.70.11312.1646051100
3.23-3.343.70.10316.639589199.7
3.34-3.463.70.08524.87600199.5
3.46-3.63.70.08615.5075781100
3.6-3.763.70.06720.645598199.8
3.76-3.963.70.05823.083585199.8
3.96-4.23.60.05127.9455961100
4.2-4.533.70.0527.7765931100
4.53-4.983.70.04530.3386191100
4.98-5.73.60.03336.38596199.7
5.7-7.173.60.03337.338612199.7
7.17-353.40.02647.56617196.3

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.77 / FOM acentric: 0.78 / FOM centric: 0.71 / Reflection: 5022 / Reflection acentric: 4428 / Reflection centric: 594
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3.6-3.90.760.750.8785579164
6.4-10.30.810.840.67709586123
5.1-6.40.790.80.75852744108
4.5-5.10.760.770.68861761100
3.9-4.50.760.770.7415171381136

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.15phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.673→20.14 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7754 / SU ML: 0.39 / σ(F): 1.35 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 1151 10.02 %
Rwork0.201 --
obs0.2051 11484 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.22 Å2 / Biso mean: 81.9439 Å2 / Biso min: 33.85 Å2
Refinement stepCycle: LAST / Resolution: 2.673→20.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2472 2 25 2499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012762
X-RAY DIFFRACTIONf_angle_d0.4094308
X-RAY DIFFRACTIONf_chiral_restr0.019568
X-RAY DIFFRACTIONf_plane_restr0.002114
X-RAY DIFFRACTIONf_dihedral_angle_d11.3851366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6732-2.79450.36421180.33581054117279
2.7945-2.94140.39481390.3221257139693
2.9414-3.12510.33021450.26281304144999
3.1251-3.36540.25221440.22161304144898
3.3654-3.70220.24751480.18831310145897
3.7022-4.23350.20741510.163613471498100
4.2335-5.31750.22611510.173813641515100
5.3175-20.14030.19691550.17671393154899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.11061.052-0.13520.8831-0.76751.5182-0.73861.40230.3415-0.528-0.03180.1217-0.6032-0.45850.58081.24930.0238-0.36251.4765-0.17060.687716.66149.9943-8.718
23.62830.22611.1725.3467-1.21780.9388-0.10270.29730.19010.10580.01990.1957-0.11630.03970.09590.62340.0244-0.18860.3289-0.06630.464714.633845.660212.1494
34.84341.5956-2.32594.79932.17444.5734-0.83830.92650.8614-0.64431.2420.37210.095-0.78150.27881.40410.0416-0.55831.6596-0.09170.723110.836150.0262-21.7703
43.0535-0.00680.98712.9871-0.50610.389-0.6597-0.0276-0.1546-0.19520.56330.0058-0.3011.52120.03411.4957-0.30370.01322.0283-0.09930.54936.744815.299450.0423
51.78320.9028-1.73812.6998-2.95473.58870.3214-0.7736-0.10930.6981-0.1749-0.0449-0.70130.78710.0030.9211-0.0804-0.09750.6205-0.00090.485828.489519.472129.9598
62.2348-1.72070.19685.804-2.44892.5524-0.0504-0.2493-0.17860.55930.20310.29630.0353-0.3017-0.12440.7165-0.0672-0.13040.3402-0.00570.387416.522323.200823.2747
72.1831-0.41852.36712.5398-0.2612.6442-0.0412-1.18090.03340.95280.35910.032-0.47551.0078-0.00061.4719-0.3737-0.20321.6357-0.04980.428334.264615.391847.799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 40 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 73 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 80 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 32 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 40 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 68 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 69 through 80 )B0

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