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- PDB-1csp: CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS MAJOR COLD SHOCK PROTE... -

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Basic information

Entry
Database: PDB / ID: 1csp
TitleCRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS MAJOR COLD SHOCK PROTEIN, CSPB: A UNIVERSAL NUCLEIC-ACID BINDING DOMAIN
ComponentsCOLD SHOCK PROTEIN B(CSPB)Cold shock response
KeywordsTRANSCRIPTION REGULATION
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
Cold shock protein CspB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsSchindelin, H. / Heinemann, U.
Citation
Journal: Nature / Year: 1993
Title: Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein.
Authors: Schindelin, H. / Marahiel, M.A. / Heinemann, U.
#1: Journal: Proteins / Year: 1992
Title: Overproduction, Crystallization, and Preliminary X-Ray Diffraction Studies of the Major Cold Shock Protein from Bacillus Subtilis, Cspb
Authors: Schindelin, H. / Herrler, M. / Willimsky, G. / Marahiel, M.A. / Heinemann, U.
History
DepositionMay 12, 1993Processing site: BNL
Revision 1.0May 12, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET STRANDS 1 TO 4 OF THE BETA-SHEET HAVE GREEK-KEY TOPOLOGY. THE SHEET FORMS A FIVE-STRANDED ...SHEET STRANDS 1 TO 4 OF THE BETA-SHEET HAVE GREEK-KEY TOPOLOGY. THE SHEET FORMS A FIVE-STRANDED BETA-BARREL WITH BULGES IN STRANDS 3 AND 5. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COLD SHOCK PROTEIN B(CSPB)


Theoretical massNumber of molelcules
Total (without water)7,3721
Polymers7,3721
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.940, 58.940, 46.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-139-

HOH

21A-140-

HOH

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Components

#1: Protein COLD SHOCK PROTEIN B(CSPB) / Cold shock response


Mass: 7372.126 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P32081
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.16 Å3/Da / Density % sol: 61.06 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 12 Å / Num. obs: 4222 / % possible obs: 97.5 % / Rmerge(I) obs: 0.055

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.45→10 Å / σ(F): 1 /
RfactorNum. reflection
obs0.195 3496
Refinement stepCycle: LAST / Resolution: 2.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms505 0 0 40 545
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.29
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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