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- PDB-3pf5: Crystal structure of Bs-CspB in complex with rU6 -

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Basic information

Entry
Database: PDB / ID: 3pf5
TitleCrystal structure of Bs-CspB in complex with rU6
Components
  • Cold shock protein cspBCold shock response
  • hexaribouracil (rU6)
KeywordsGENE REGULATION/RNA / BETA BARREL / PROTEIN-RNA complex / COLD SHOCK RESPONSE / TRANSCRIPTION REGULATION / TRANSLATION REGULATION / OB fold / cold shock domain / RNA/DNA binding / single-stranded RNA and DNA / cytosol / GENE REGULATION-RNA complex
Function / homology
Function and homology information


nucleoid / regulation of gene expression / nucleic acid binding / DNA binding / cytoplasm
Similarity search - Function
Cold shock, CspA / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Cold shock, CspA / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / Cold shock protein CspB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSachs, R. / Max, K.E.A. / Heinemann, U.
CitationJournal: Rna / Year: 2012
Title: RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution.
Authors: Sachs, R. / Max, K.E. / Heinemann, U. / Balbach, J.
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Sep 6, 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_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: Cold shock protein cspB
B: Cold shock protein cspB
R: hexaribouracil (rU6)
S: hexaribouracil (rU6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3535
Polymers18,3284
Non-polymers241
Water3,207178
1
A: Cold shock protein cspB
S: hexaribouracil (rU6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1883
Polymers9,1642
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-6 kcal/mol
Surface area4660 Å2
MethodPISA
2
B: Cold shock protein cspB
R: hexaribouracil (rU6)


Theoretical massNumber of molelcules
Total (without water)9,1642
Polymers9,1642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-7 kcal/mol
Surface area5190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.038, 49.769, 57.380
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 Cold shock protein cspB / Cold shock response / Major cold shock protein


Mass: 7372.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU09100, cspA, cspB / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P32081
#2: RNA chain hexaribouracil (rU6)


Mass: 1792.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.91 Å3/Da / Density % sol: 35.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein buffer: 50mM TRIS, 20mM Na-HEPES, pH 7.5; Bs-CspB.rU6 complex concentration: 70mg/ml; crystallization buffer: 31% PEG 3350, 0.25M MgCl2, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING ...Details: protein buffer: 50mM TRIS, 20mM Na-HEPES, pH 7.5; Bs-CspB.rU6 complex concentration: 70mg/ml; crystallization buffer: 31% PEG 3350, 0.25M MgCl2, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 12, 2009 / Details: mirrors, slits
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→17.5 Å / Num. all: 15961 / Num. obs: 15961 / % possible obs: 96.08 % / Observed criterion σ(I): -3 / Redundancy: 2.87 % / Biso Wilson estimate: 25.148 Å2 / Rsym value: 0.079 / Net I/σ(I): 10.48
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 2.84 % / Mean I/σ(I) obs: 1.85 / Num. unique all: 1033 / Rsym value: 0.545 / % possible all: 93.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CSP

1csp


Resolution: 1.68→17.46 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.445 / SU ML: 0.081 / Isotropic thermal model: ISOTROPIC + TLS / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23466 798 5 %RANDOM
Rwork0.1798 ---
all0.18252 15162 --
obs0.18252 15162 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.765 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--1.65 Å20 Å2
3----1.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.217 Å
Refinement stepCycle: LAST / Resolution: 1.68→17.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 117 1 178 1332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221219
X-RAY DIFFRACTIONr_bond_other_d0.0040.02791
X-RAY DIFFRACTIONr_angle_refined_deg1.4592.0621673
X-RAY DIFFRACTIONr_angle_other_deg0.98131949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3326.20758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61915186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.603152
X-RAY DIFFRACTIONr_chiral_restr0.0680.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021311
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02245
X-RAY DIFFRACTIONr_nbd_refined0.1870.2178
X-RAY DIFFRACTIONr_nbd_other0.1730.2797
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2585
X-RAY DIFFRACTIONr_nbtor_other0.0860.2658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2127
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.215
X-RAY DIFFRACTIONr_mcbond_it1.0932862
X-RAY DIFFRACTIONr_mcbond_other0.2832286
X-RAY DIFFRACTIONr_mcangle_it1.34131064
X-RAY DIFFRACTIONr_scbond_it2.6034.5654
X-RAY DIFFRACTIONr_scangle_it3.4656601
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 56
Rwork0.22 1071

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