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- PDB-5xtm: Crystal structure of PhoRpp38 bound to a K-turn in P12.2 helix -

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Basic information

Entry
Database: PDB / ID: 5xtm
TitleCrystal structure of PhoRpp38 bound to a K-turn in P12.2 helix
Components
  • 50S ribosomal protein L7AeRibosome
  • RNA (47-MER)
KeywordsRNA BINDING PROTEIN/RNA / RNA-Protein Complex / Rnase P / Kink turn / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / 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 speciesPyrococcus horikoshii (archaea)
Pyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOshima, K. / Kimura, M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif.
Authors: Oshima, K. / Gao, X. / Hayashi, S. / Ueda, T. / Nakashima, T. / Kimura, M.
History
DepositionJun 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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 / struct_conn_type
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.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_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S ribosomal protein L7Ae
B: RNA (47-MER)
C: 50S ribosomal protein L7Ae
D: RNA (47-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,80628
Polymers60,2224
Non-polymers58324
Water5,513306
1
A: 50S ribosomal protein L7Ae
B: RNA (47-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,42715
Polymers30,1112
Non-polymers31613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-115 kcal/mol
Surface area13040 Å2
MethodPISA
2
C: 50S ribosomal protein L7Ae
D: RNA (47-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,37913
Polymers30,1112
Non-polymers26711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-90 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.070, 71.720, 91.280
Angle α, β, γ (deg.)90.000, 105.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 50S ribosomal protein L7Ae / Ribosome / Ribonuclease P protein component Rpp38 / RNase P component Rpp38 / Ribosomal protein L8e


Mass: 14645.026 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: rpl7ae, PH1496 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62009
#2: RNA chain RNA (47-MER)


Mass: 15466.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pyrococcus horikoshii OT3 (archaea)
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Na-Cacodylate, PEG 400, Mg-Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→39.26 Å / Num. obs: 37804 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.684 % / Biso Wilson estimate: 34.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.096 / Χ2: 0.928 / Net I/σ(I): 13.7 / Num. measured all: 177058
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.234.6640.7682.1528014610460070.7230.86898.4
2.23-2.384.7150.5093.1626929571957110.8790.57499.9
2.38-2.574.7220.3674.3125182533653330.9230.41399.9
2.57-2.814.7360.2176.9923205491049000.9730.24599.8
2.81-3.144.7190.10813.5521061447244630.9910.12199.8
3.14-3.634.6910.05923.6318497395639430.9970.06699.7
3.63-4.434.6540.0434.0115557335633430.9980.04599.6
4.43-6.234.6120.03437.3411972260225960.9980.03999.8
6.23-39.264.4040.02543.296641152915080.9990.02998.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2czw

2czw


Resolution: 2.1→39.264 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1876 4.96 %
Rwork0.1969 35910 -
obs0.1981 37786 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.84 Å2 / Biso mean: 37.215 Å2 / Biso min: 18.03 Å2
Refinement stepCycle: final / Resolution: 2.1→39.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 2054 24 306 4251
Biso mean--56.9 39.81 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024193
X-RAY DIFFRACTIONf_angle_d0.5816145
X-RAY DIFFRACTIONf_chiral_restr0.037770
X-RAY DIFFRACTIONf_plane_restr0.004422
X-RAY DIFFRACTIONf_dihedral_angle_d20.5151875
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0999-2.15670.33781400.31842676281697
2.1567-2.22010.36531400.293327342874100
2.2201-2.29180.27551460.274227672913100
2.2918-2.37370.27231470.254527632910100
2.3737-2.46870.2841350.25527722907100
2.4687-2.5810.28141470.249127402887100
2.581-2.71710.29921450.251427632908100
2.7171-2.88730.25051430.252627702913100
2.8873-3.11010.271490.2227452894100
3.1101-3.42290.21621470.191327792926100
3.4229-3.91790.17341380.158427692907100
3.9179-4.93460.16811480.14327882936100
4.9346-39.27060.17921510.154928442995100

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