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- PDB-3i2z: Structure of cold shock protein E from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 3i2z
TitleStructure of cold shock protein E from Salmonella typhimurium
ComponentsRNA chaperone, negative regulator of cspA transcription
KeywordsGENE REGULATION / BETA BARREL / DNA BINDING PROTEIN/TRANSCRIPTION / Cytoplasm
Function / homology
Function and homology information


negative regulation of termination of DNA-templated transcription / transcription antitermination factor activity, RNA binding / regulation of gene expression / nucleic acid binding / 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 domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold ...Cold shock, CspA / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / 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 chaperone, negative regulator of cspA transcription
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMorgan, H.P. / McNae, I. / Wear, M.A. / Gallagher, M. / Walkinshaw, M.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and X-ray structure of cold-shock protein E from Salmonella typhimurium
Authors: Morgan, H.P. / Wear, M.A. / McNae, I. / Gallagher, M.P. / Walkinshaw, M.D.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA chaperone, negative regulator of cspA transcription
A: RNA chaperone, negative regulator of cspA transcription


Theoretical massNumber of molelcules
Total (without water)15,3712
Polymers15,3712
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA chaperone, negative regulator of cspA transcription


Theoretical massNumber of molelcules
Total (without water)7,6861
Polymers7,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: RNA chaperone, negative regulator of cspA transcription


Theoretical massNumber of molelcules
Total (without water)7,6861
Polymers7,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.395, 46.798, 46.718
Angle α, β, γ (deg.)90.00, 103.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA chaperone, negative regulator of cspA transcription / CSPE / cold shock protein E


Mass: 7685.595 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: 1344 / Description: T7 expression - pET vector was used / Gene: cold shock protein E, cspE / Plasmid: pET28a_CspE / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3) / References: UniProt: Q7CQZ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 28% PEG 20000, 0.05M AMPSO, 1% glycerol, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.074 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2006 / Details: Mirrors
RadiationMonochromator: a double crystal Si(III,)with horizontal saggital focusing system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 1.1→45.36 Å / Num. obs: 47339 / % possible obs: 99.82 % / Observed criterion σ(F): 1.1 / Observed criterion σ(I): 1.1 / Redundancy: 5 % / Rmerge(I) obs: 0.047 / Num. measured all: 260904
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.8 / Num. unique all: 7261 / Rsym value: 0.41 / % possible all: 100

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1MJC; A decapeptide (residues 12-21) from the E. coli cold shock protein A

1mjc


Resolution: 1.1→11.21 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.514 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23424 2532 5.1 %RANDOM
Rwork0.20354 ---
obs0.20506 47339 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.862 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.92 Å2
2--1.8 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 1.1→11.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 0 100 1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221098
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.921479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0585140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87625.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25915185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.446152
X-RAY DIFFRACTIONr_chiral_restr0.3120.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02846
X-RAY DIFFRACTIONr_nbd_refined0.2160.2435
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3840.216
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 196 -
Rwork0.349 3476 -
obs--100 %

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