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- PDB-5jx4: Crystal structure of E36-G37del mutant of the Bacillus caldolytic... -

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Basic information

Entry
Database: PDB / ID: 5jx4
TitleCrystal structure of E36-G37del mutant of the Bacillus caldolyticus cold shock protein.
ComponentsCold shock protein CspBCold shock response
KeywordsDNA BINDING PROTEIN / BcCSP / monomer / mutant / cold shock protein.
Function / homology
Function and homology information


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
Cold shock protein CspB
Similarity search - Component
Biological speciesBacillus caldolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCarvajal, A. / Castro-Fernandez, V. / Cabrejos, D. / Fuentealba, M. / Pereira, H.M. / Vallejos, G. / Cabrera, R. / Garratt, R.C. / Komives, E.A. / Ramirez-Sarmiento, C.A. / Babul, J.
Funding support Chile, 2items
OrganizationGrant numberCountry
FONDECYT1130510 Chile
FONDEQUIPEQM120208 Chile
CitationJournal: FEBS J. / Year: 2017
Title: Unusual dimerization of a BcCsp mutant leads to reduced conformational dynamics.
Authors: Carvajal, A.I. / Vallejos, G. / Komives, E.A. / Castro-Fernandez, V. / Leonardo, D.A. / Garratt, R.C. / Ramirez-Sarmiento, C.A. / Babul, J.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Sep 27, 2023Group: 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

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Assembly

Deposited unit
A: Cold shock protein CspB
B: Cold shock protein CspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1817
Polymers14,7002
Non-polymers4805
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint1 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.009, 44.077, 36.484
Angle α, β, γ (deg.)90.000, 99.280, 90.000
Int Tables number4
Space group name H-MP1211
DetailsDimer confirmed by gel filtration

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Components

#1: Protein Cold shock protein CspB / Cold shock response


Mass: 7350.220 Da / Num. of mol.: 2 / Mutation: E36del, G37del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus caldolyticus (bacteria) / Gene: cspB / Plasmid: pET28b modified / Details (production host): TEV cleavage site / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)C41 / References: UniProt: P41016
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.84 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium Acetate, Poly(ethylene glycol) methyl ether 2000 30%, 0.2 M Ammonium Sulfate. Protein 20 mg/mL in 20 mM Sodium phosphate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→18.8 Å / Num. obs: 9547 / % possible obs: 95.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 5.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.114 / % possible all: 70.3

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HAX

2hax


Resolution: 1.8→18.797 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.6
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 462 4.86 %Random selection
Rwork0.15 ---
obs0.1515 9514 95.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 40.26 Å2 / Biso mean: 9.2329 Å2 / Biso min: 0.92 Å2
Refinement stepCycle: final / Resolution: 1.8→18.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 25 221 1282
Biso mean--22.81 16.21 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131093
X-RAY DIFFRACTIONf_angle_d1.3351471
X-RAY DIFFRACTIONf_chiral_restr0.047144
X-RAY DIFFRACTIONf_plane_restr0.005194
X-RAY DIFFRACTIONf_dihedral_angle_d13.958388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-2.05910.19751570.14482791294889
2.0591-2.59310.18221840.15123052323697
2.5931-18.79810.17151210.15163209333099

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