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- PDB-5d6g: CRYSTAL STRUCTURE OF FRAGMENT OF RIBOSOMAL PROTEIN P0 IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 5d6g
TitleCRYSTAL STRUCTURE OF FRAGMENT OF RIBOSOMAL PROTEIN P0 IN COMPLEX WITH 74NT 23S RNA FROM METHANOCOCCUS JANNASCHII
Components
  • 23S ribosomal RNA
  • 50S ribosomal protein L10
KeywordsTRANSLATION / Archaeal Proteins / Methanococcus / Protein Structure / RNA / Ribosomal Proteins / Ribosomes
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / structural constituent of ribosome
Similarity search - Function
Ribosomal protein L10, N-terminal fragment, domain II / Ribosomal protein L10, N-terminal RNA-binding domain / Molybdopterin biosynthesis moea protein, domain 2 / 50S ribosomal protein L10, archaea / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 ...Ribosomal protein L10, N-terminal fragment, domain II / Ribosomal protein L10, N-terminal RNA-binding domain / Molybdopterin biosynthesis moea protein, domain 2 / 50S ribosomal protein L10, archaea / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / : / Large ribosomal subunit protein uL10
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF FRAGMENT OF RIBOSOMAL PROTEIN P0 IN COMPLEX WITH 74NT 23S RNA FROM METHANOCOCCUS JANNASCHII
Authors: Gabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B.
History
DepositionAug 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L10
0: 23S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3314
Polymers47,2822
Non-polymers492
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-35 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.230, 108.310, 112.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein 50S ribosomal protein L10 / / Acidic ribosomal protein P0 homolog / MjaL10


Mass: 23353.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rpl10, rplP0, MJ0509 / Plasmid: pET-11c/MjaP0NTF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54049
#2: RNA chain 23S ribosomal RNA /


Mass: 23928.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pMja23S-74.UC18 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1(Blue) / References: REF: 470491724
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Sodium Cacodylate, pH 6.5, 0.2 M KCl, 0.1 M Magnesium acetate, 9% PEG 6000, 0.5 mM CTAB

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 49425 / Num. obs: 10828 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.56 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 7.15
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.94 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JSY

3jsy


Resolution: 3.3→24.827 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 2.36 / Phase error: 34.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2985 487 4.98 %
Rwork0.245 --
obs0.2475 9780 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→24.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 1588 2 5 3167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093378
X-RAY DIFFRACTIONf_angle_d1.4354935
X-RAY DIFFRACTIONf_dihedral_angle_d15.6971527
X-RAY DIFFRACTIONf_chiral_restr0.059629
X-RAY DIFFRACTIONf_plane_restr0.01348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.77630.36971580.3173018X-RAY DIFFRACTION98
3.7763-4.75220.33031610.27623080X-RAY DIFFRACTION99
4.7522-24.8280.24991680.2023195X-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)
12.72320.2497-0.74943.1339-1.48531.6687-0.3242-0.42640.47242.52960.46790.46010.50280.5485-0.58451.37880.2157-0.13180.9284-0.49371.9421141.849813.273239.0647
26.3154-1.4387-6.93783.070.38831.99490.0976-0.74521.4952-1.54450.24420.62631.9478-0.0068-0.09920.97020.10060.06510.6948-0.11931.95124.925227.139738.0574
30.9094-0.7942-0.80091.5211.32941.9712-0.3912-0.55910.9171.6216-0.3607-0.49070.8875-0.99160.88052.2061-0.0020.20321.1649-0.43911.7473116.203438.283458.7273
40.5042-0.38450.93255.98982.14272.81570.4132-0.7472-0.06832.7104-0.319-2.14841.3373-1.3312-0.22092.6525-0.44990.53041.1093-0.62521.0446120.543326.293858.3613
50.53960.41281.38260.69130.56631.8412-0.5143-0.58940.79570.059-0.95950.7094-0.6837-0.47031.25371.6749-0.00940.12941.0544-0.59261.9334126.959532.584250.8643
60.66760.86941.35984.43131.68863.70970.3617-0.16741.05350.6564-0.9793-0.8157-0.6031-0.4090.68871.2185-0.15930.08310.7277-0.15491.6953129.636229.428140.6596
78.4021-0.09590.45292.01590.89260.0895-0.14040.8181-0.11940.95880.56430.8670.35370.1378-0.261.6634-0.038-0.49171.27470.46254.2681149.104214.92442.1925
82.2066-2.33622.0152.6665-0.81551.66490.1101-0.7689-0.61910.1273-0.1693-0.10970.5249-0.26740.06871.0632-0.21960.38450.69590.0421.5388117.037510.600337.3931
92.47982.0891.13312.5403-0.37582.64410.33990.2344-1.7234-0.2689-0.0913-0.1461.5157-0.174-0.0261.282-0.0273-0.12570.6349-0.14591.8377122.20432.480930.52
100.74930.461-1.43993.91660.17561.285-0.32330.07890.2716-0.80070.5105-0.34840.12630.1648-0.1730.9462-0.0807-0.06460.80950.06191.6991112.379424.818925.4017
113.3866-1.574-0.58954.29121.91585.6638-0.8761.62611.2767-1.140.0765-1.1282-0.0799-0.14260.70781.1755-0.1227-0.20631.01380.51031.0989116.955352.830320.6687
12-0.05480.032-0.95886.8595-0.73042.0834-0.19540.00270.3387-0.4221-0.6113-0.3456-0.41280.02720.51571.0301-0.1026-0.35130.9123-0.13091.1923115.345333.443821.1982
131.5841.7695-2.14432.3439-1.46185.81160.6003-1.451-3.3755-0.058-0.2013-0.4601-1.903-1.0484-0.83411.9439-0.163-0.59031.8339-0.11861.5991110.445210.744316.2968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 0 and resid 1151:1162
2X-RAY DIFFRACTION2chain 0 and resid 1163:1167
3X-RAY DIFFRACTION3chain 0 and resid 1168:1182
4X-RAY DIFFRACTION4chain 0 and resid 1183:1194
5X-RAY DIFFRACTION5chain 0 and resid 1195:1204
6X-RAY DIFFRACTION6chain 0 and resid 1205:1221
7X-RAY DIFFRACTION7chain 0 and resid 1222:1224
8X-RAY DIFFRACTION8chain A and resid 10:52
9X-RAY DIFFRACTION9chain A and resid 53:85
10X-RAY DIFFRACTION10chain A and resid 86:137
11X-RAY DIFFRACTION11chain A and resid 138:155
12X-RAY DIFFRACTION12chain A and resid 156:201
13X-RAY DIFFRACTION13chain A and resid 202:214

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