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- PDB-1mjc: CRYSTAL STRUCTURE OF CSPA, THE MAJOR COLD SHOCK PROTEIN OF ESCHER... -

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Basic information

Entry
Database: PDB / ID: 1mjc
TitleCRYSTAL STRUCTURE OF CSPA, THE MAJOR COLD SHOCK PROTEIN OF ESCHERICHIA COLI
ComponentsMAJOR COLD-SHOCK PROTEIN 7.4
KeywordsTRANSCRIPTION REGULATION
Function / homology
Function and homology information


negative regulation of termination of DNA-templated transcription / transcription antitermination factor activity, RNA binding / response to cold / single-stranded DNA binding / regulation of gene expression / nucleic acid binding / single-stranded RNA binding / positive regulation of DNA-templated transcription / DNA binding / RNA binding / cytosol
Similarity search - Function
Cold shock, CspA / : / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins ...Cold shock, CspA / : / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / 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 CspA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsSchindelin, H. / Heinemann, U.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal structure of CspA, the major cold shock protein of Escherichia coli.
Authors: Schindelin, H. / Jiang, W. / Inouye, M. / Heinemann, U.
#1: 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. / Heinemann, U.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Major Cold Shock Protein of Escherichia Coli
Authors: Goldstein, J. / Pollitt, N.S. / Inouye, M.
History
DepositionMar 18, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: 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 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: MAJOR COLD-SHOCK PROTEIN 7.4


Theoretical massNumber of molelcules
Total (without water)7,2801
Polymers7,2801
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.120, 39.920, 30.920
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 MAJOR COLD-SHOCK PROTEIN 7.4


Mass: 7280.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: S2 / References: UniProt: P0A9X9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2 Å3/Da / Density % sol: 38.4 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNaCl
426 %PEG15001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 3785 / % possible obs: 88.9 % / Num. measured all: 15912 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.13 Å / % possible obs: 87.8 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 5.99

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.187 -
obs0.187 3774
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms514 0 0 36 550
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.312
X-RAY DIFFRACTIONx_mcangle_it4.133
X-RAY DIFFRACTIONx_scbond_it3.434.5
X-RAY DIFFRACTIONx_scangle_it5.294.5
Refinement
*PLUS
Rfactor obs: 0.187 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.047
X-RAY DIFFRACTIONx_planar_d0.050.049
X-RAY DIFFRACTIONx_plane_restr0.0150.009
X-RAY DIFFRACTIONx_chiral_restr0.150.106

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