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- PDB-3v7q: Crystal structure of B. subtilis YlxQ at 1.55 A resolution -

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Basic information

Entry
Database: PDB / ID: 3v7q
TitleCrystal structure of B. subtilis YlxQ at 1.55 A resolution
ComponentsProbable ribosomal protein ylxQ
KeywordsRNA BINDING PROTEIN / L7Ae superfamily / K-turn binding / K-turn RNA / Hypothetical ribosomal protein
Function / homology
Function and homology information


ribosome biogenesis / ribonucleoprotein complex / RNA binding
Similarity search - Function
Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / 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
CITRIC ACID / : / RNA-binding protein YlxQ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBaird, N.J. / Zhang, J. / Hamma, T. / Ferre-D'Amare, A.R.
CitationJournal: Rna / Year: 2012
Title: YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.
Authors: Baird, N.J. / Zhang, J. / Hamma, T. / Ferre-D'Amare, A.R.
History
DepositionDec 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ribosomal protein ylxQ
B: Probable ribosomal protein ylxQ
C: Probable ribosomal protein ylxQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0428
Polymers33,3873
Non-polymers6555
Water4,432246
1
A: Probable ribosomal protein ylxQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3603
Polymers11,1291
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable ribosomal protein ylxQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3603
Polymers11,1291
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Probable ribosomal protein ylxQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3212
Polymers11,1291
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.407, 61.291, 94.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable ribosomal protein ylxQ


Mass: 11128.995 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU16620, rplGA, ylxQ, ymxC / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P32729
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium acetate pH 7.0, 0.1 M sodium citrate pH 5.6, and 30% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 10, 2010
RadiationMonochromator: Asymmetric curved crystal of Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 42151 / Num. obs: 41302 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.6 Å2
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5.5 % / Num. unique all: 4152 / % possible all: 98.4

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3on1

3on1


Resolution: 1.55→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 149294.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4152 10 %RANDOM
Rwork0.2 ---
obs0.2 41302 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8237 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2---7.1 Å20 Å2
3---6.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.55→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 34 246 2529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it4.271.5
X-RAY DIFFRACTIONc_mcangle_it5.862
X-RAY DIFFRACTIONc_scbond_it8.632
X-RAY DIFFRACTIONc_scangle_it11.42.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.55→1.56 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 77 10.4 %
Rwork0.253 5473 -
obs-646 86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6cit.parcit.top

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