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- PDB-6hct: Crystal structure of Archeoglobus fulgidus L7Ae bound to its cogn... -

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Basic information

Entry
Database: PDB / ID: 6hct
TitleCrystal structure of Archeoglobus fulgidus L7Ae bound to its cognate UTR k-turn
Components
  • 50S ribosomal protein L7Ae
  • RNA (5'-R(*GP*CP*CP*GP*AP*UP*GP*AP*AP*UP*G)-3')
  • RNA (5'-R(*GP*CP*CP*GP*AP*UP*GP*AP*AP*UP*GP*CP*AP*UP*GP*AP*AP*GP*C)-3')
  • RNA (5'-R(P*CP*AP*UP*GP*AP*AP*GP*C)-3')
KeywordsRNA / Gene regulation / RNA structure / kink-turn / X-ray crystallography
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L30/S12 / Ribosomal protein L7Ae, archaea / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like ...Ribosomal protein L30/S12 / Ribosomal protein L7Ae, archaea / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Archaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.091 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
CitationJournal: RNA / Year: 2019
Title: The role of RNA structure in translational regulation by L7Ae protein in archaea.
Authors: Huang, L. / Ashraf, S. / Lilley, D.M.J.
History
DepositionAug 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*CP*GP*AP*UP*GP*AP*AP*UP*GP*CP*AP*UP*GP*AP*AP*GP*C)-3')
B: RNA (5'-R(*GP*CP*CP*GP*AP*UP*GP*AP*AP*UP*GP*CP*AP*UP*GP*AP*AP*GP*C)-3')
C: 50S ribosomal protein L7Ae
D: 50S ribosomal protein L7Ae
E: RNA (5'-R(*GP*CP*CP*GP*AP*UP*GP*AP*AP*UP*G)-3')
F: RNA (5'-R(P*CP*AP*UP*GP*AP*AP*GP*C)-3')
G: 50S ribosomal protein L7Ae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,29812
Polymers57,1107
Non-polymers1885
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-68 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.140, 142.140, 166.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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RNA chain , 3 types, 4 molecules ABEF

#1: RNA chain RNA (5'-R(*GP*CP*CP*GP*AP*UP*GP*AP*AP*UP*GP*CP*AP*UP*GP*AP*AP*GP*C)-3')


Mass: 6140.737 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Archaeoglobus fulgidus DSM 4304 (archaea)
#3: RNA chain RNA (5'-R(*GP*CP*CP*GP*AP*UP*GP*AP*AP*UP*G)-3')


Mass: 3546.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Production host: Escherichia coli BL21(DE3) (bacteria)
#4: RNA chain RNA (5'-R(P*CP*AP*UP*GP*AP*AP*GP*C)-3')


Mass: 2549.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Archaeoglobus fulgidus DSM 4304 (archaea)

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Protein , 1 types, 3 molecules CDG

#2: Protein 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 12910.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Gene: rpl7ae, AF_0764 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold (DE3) pLysS / References: UniProt: O29494

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Non-polymers , 2 types, 5 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.01 M Magnesium Acetate, 0.05 M MES pH 5.6, 2.5 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91962 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91962 Å / Relative weight: 1
ReflectionResolution: 3.09→83.4 Å / Num. obs: 16002 / % possible obs: 99.97 % / Redundancy: 10.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.028 / Net I/σ(I): 13.9
Reflection shellResolution: 3.09→3.14 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.914 / Num. unique obs: 785 / CC1/2: 0.382 / Rpim(I) all: 0.291 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bw0

4bw0


Resolution: 3.091→71.07 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.98
RfactorNum. reflection% reflection
Rfree0.2366 775 4.9 %
Rwork0.1866 --
obs0.1891 15829 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.091→71.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 1221 9 0 3926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114118
X-RAY DIFFRACTIONf_angle_d1.6215841
X-RAY DIFFRACTIONf_dihedral_angle_d7.9182859
X-RAY DIFFRACTIONf_chiral_restr0.081719
X-RAY DIFFRACTIONf_plane_restr0.009535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0906-3.28430.38111410.3052403X-RAY DIFFRACTION97
3.2843-3.53780.33791330.26272452X-RAY DIFFRACTION99
3.5378-3.89380.28421080.21552482X-RAY DIFFRACTION99
3.8938-4.45720.22261110.1712529X-RAY DIFFRACTION99
4.4572-5.61530.1951490.16992520X-RAY DIFFRACTION100
5.6153-71.08880.21681330.16452668X-RAY DIFFRACTION99
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)
18.4298-0.9479-4.17152.23460.28893.0433-0.42090.91460.85740.55590.5818-0.3031.0163-2.1041-0.01650.7417-0.2636-0.08831.16780.20970.9626-4.670535.695238.2255
22.87030.7680.91130.75610.00712.3202-0.0113-0.3188-0.09390.0959-0.1862-0.2756-0.0897-0.96620.28270.72350.0314-0.00390.85530.02390.881810.256342.291847.2348
34.5054-0.40823.60013.6027-0.35828.4689-0.15850.0227-0.8125-0.9728-0.1505-0.6748-0.8871-1.3952-0.03880.91610.2155-0.04150.82370.0680.99054.259659.829345.0486
45.0018-2.00986.12213.311-3.74679.1520.15420.4868-1.7116-1.10531.30221.6134-0.9082-1.73-0.94831.13190.3260.01871.2090.29431.0957-2.784260.542850.1688
50.6155-1.0648-0.14672.85750.57810.09910.29020.2743-0.5173-0.37-0.43310.392-0.0083-0.43960.06890.81990.0944-0.02140.76260.09460.773310.489946.17146.9544
64.14711.815-1.79231.42340.67455.6204-0.0761-1.28720.10131.2146-1.09140.863-0.1845-1.24450.53660.8775-0.2182-0.07641.44530.11730.9879-1.191733.665145.9447
78.7702-2.8933-3.34129.5267-1.61632.10210.24110.5198-1.80140.7747-0.7541-1.6745-0.61241.0580.76391.5496-0.13890.12161.6357-0.31991.302513.595628.514915.7932
80.26151.01660.43617.75680.30341.52641.09830.9544-2.39540.5630.14241.44451.3886-1.4784-0.8571.0562-0.2414-0.73851.4477-0.42632.09847.939717.83129.5155
92.5715-0.673-1.93972.7329-0.85172.16690.17360.25552.26751.79820.70910.8695-0.24660.8151-0.35410.5392-0.13-0.05360.7314-0.1120.903617.446431.310834.6102
104.19360.02821.69651.769-0.34862.8820.33511.6202-1.1180.01470.07130.47820.88750.5922-0.26130.97150.036-0.1761.3554-0.25651.071715.928831.045626.1341
114.54970.4591-0.6494.1092-0.48563.92560.03692.3258-1.2495-0.8890.1585-0.03691.26810.00160.12830.888-0.0131-0.13141.5484-0.55151.088810.171525.798924.8793
127.80360.5497-2.23238.2715-3.36946.67730.41641.5026-1.53231.4197-0.0074-0.03610.6361-0.5401-0.79490.6979-0.2188-0.14041.0642-0.0371.30442.452228.106633.5405
134.3849-1.88-4.46550.97261.32786.5014-0.5509-1.4416-1.27590.7705-0.3167-0.3332.48220.80150.14571.2893-0.6225-0.83480.1471-0.55892.272814.831516.954834.032
140.737-0.0610.07630.8418-1.65593.2271-0.39941.2924-2.80820.70420.18711.24920.8182-0.54380.68781.78180.6957-0.10691.6648-0.76261.656617.863912.857823.0596
154.2896-0.4148-0.45523.64380.03993.2917-0.4088-0.80810.48291.10730.4906-0.1918-0.6246-0.2482-0.23421.39460.1907-00.8044-0.12590.936711.074265.205569.8668
167.6763.14170.24643.60653.81656.0206-0.82640.3784-0.47920.46960.7961.1311.31510.47340.13260.88410.17760.06510.6473-0.0240.748714.227351.414462.539
171.6367-0.47770.01965.60890.84483.9762-0.6228-0.2799-0.14281.63550.63330.96780.7557-0.4908-0.11591.13960.30450.31140.95480.15620.99728.58854.518868.3177
181.7656-3.0752-2.2468.9560.64285.8989-0.351-1.7173-1.3112.2347-0.0832-1.35740.58710.39610.8711.58530.170.00851.26190.36920.937914.310249.502173.6468
193.5398-1.7310.60915.05021.28493.4991-0.3765-0.4282-0.191.30890.6618-0.0271-0.9452-0.5162-0.16911.19670.36930.08530.7842-0.01140.821610.809862.339466.2579
207.22230.4836-2.83720.47550.73062.857-0.2184-2.28051.6020.21390.0841-0.3686-1.3010.24270.23851.53980.3124-0.34321.5287-0.28971.166920.555866.808376.7368
211.8628-1.5973-0.91122.20621.64520.81080.2395-0.64330.7244-0.1850.1918-0.3686-0.41710.6308-0.16710.7399-0.33810.00261.24970.01420.9008-26.881433.375847.6009
227.47641.9883-0.41412.11910.42571.42310.79851.2627-0.5962-0.1304-0.1867-0.333-0.18160.85-0.77920.6703-0.04780.03511.1962-0.02480.9143-30.664427.780246.4548
236.70963.5049-1.87551.8645-0.61964.21941.84510.8196-1.8379-0.353-1.04630.1301-0.3562-1.00670.01992.2782-0.31330.54921.1855-0.47891.6454-37.036737.101374.4293
244.5214-1.19916.54583.2530.24392.03130.6326-0.22090.38280.7542-0.4882-1.01630.67752.666-0.67350.832-0.5252-0.2461.7037-0.1491.0281-27.173822.981568.5004
253.74783.25341.00733.89440.17852.2957-1.21281.06491.6379-1.3432-0.68180.3665-0.3428-1.86151.38740.6429-0.0817-0.00151.1367-0.19980.8808-40.173827.870558.0288
263.6441-0.3365-0.01393.2978-1.06654.70650.2751-1.00581.11090.49530.2243-0.1142-0.61820.8467-0.29460.9503-0.3505-0.02751.1213-0.19720.8387-34.891431.943765.2639
274.45670.14510.40392.67150.98154.8273-0.58611.012-0.844-0.04640.9086-1.06752.08941.0826-0.63110.92890.1712-0.06791.11490.08240.7731-33.018517.808965.8978
285.19033.96532.57494.05573.55893.63850.8496-2.7323-1.53320.9133-1.2231-0.7484-0.20651.9311-0.26331.3514-0.55310.14181.68890.10520.8853-35.230820.485177.7983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 15 )
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 19 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 19 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 8 )
8X-RAY DIFFRACTION8chain 'C' and (resid 9 through 31 )
9X-RAY DIFFRACTION9chain 'C' and (resid 32 through 40 )
10X-RAY DIFFRACTION10chain 'C' and (resid 41 through 68 )
11X-RAY DIFFRACTION11chain 'C' and (resid 69 through 85 )
12X-RAY DIFFRACTION12chain 'C' and (resid 86 through 93 )
13X-RAY DIFFRACTION13chain 'C' and (resid 94 through 103 )
14X-RAY DIFFRACTION14chain 'C' and (resid 104 through 117 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 31 )
16X-RAY DIFFRACTION16chain 'D' and (resid 32 through 40 )
17X-RAY DIFFRACTION17chain 'D' and (resid 41 through 61 )
18X-RAY DIFFRACTION18chain 'D' and (resid 62 through 68 )
19X-RAY DIFFRACTION19chain 'D' and (resid 69 through 103 )
20X-RAY DIFFRACTION20chain 'D' and (resid 104 through 117 )
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 11 )
22X-RAY DIFFRACTION22chain 'F' and (resid 12 through 19 )
23X-RAY DIFFRACTION23chain 'G' and (resid 1 through 8 )
24X-RAY DIFFRACTION24chain 'G' and (resid 9 through 31 )
25X-RAY DIFFRACTION25chain 'G' and (resid 32 through 40 )
26X-RAY DIFFRACTION26chain 'G' and (resid 41 through 93 )
27X-RAY DIFFRACTION27chain 'G' and (resid 94 through 103 )
28X-RAY DIFFRACTION28chain 'G' and (resid 104 through 117 )

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