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- PDB-6t00: Crystal structure of Cold Shock Protein B (CSP-B) containing 4-F-... -

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Basic information

Entry
Database: PDB / ID: 6t00
TitleCrystal structure of Cold Shock Protein B (CSP-B) containing 4-F-Phe modified residues
ComponentsCold shock protein CspDCold shock response
KeywordsSTRUCTURAL PROTEIN / fluorine cold shock protein
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, OB-fold
Similarity search - Domain/homology
Cold shock protein CspD / Cold shock protein CspB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhou, T. / Mayans, O.
CitationJournal: Sci Rep / Year: 2020
Title: What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein.
Authors: Welte, H. / Zhou, T. / Mihajlenko, X. / Mayans, O. / Kovermann, M.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 CspD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7263
Polymers7,4271
Non-polymers2992
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint2 kcal/mol
Surface area4740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.940, 54.940, 57.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Cold shock protein CspD / Cold shock response / Cold-shock protein / Cold-shock protein CspB / Major cold shock protein / Putative cold-shock DNA- ...Cold-shock protein / Cold-shock protein CspB / Major cold shock protein / Putative cold-shock DNA-binding protein


Mass: 7426.987 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: B4122_0412, B4417_4327, CJ481_22435, DFO69_3150, ETA10_05025, ETK61_05130, ETL41_18150, FA024_03420, SC09_Contig19orf00064
Production host: Escherichia coli (E. coli) / References: UniProt: A0A063XII3, UniProt: P32081*PLUS
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM CHES/ Sodium hydroxide pH 9.5, 1000 mM Sodium citrate tribasic

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→39.79 Å / Num. obs: 5551 / % possible obs: 99.9 % / Redundancy: 12.43 % / CC1/2: 0.999 / Rsym value: 0.087 / Net I/σ(I): 17.23
Reflection shellResolution: 2.1→2.2 Å / Num. unique obs: 692 / CC1/2: 0.429 / Rsym value: 2.252

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1csp

1csp


Resolution: 2.1→39.79 Å / SU ML: 0.2781 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.9329
RfactorNum. reflection% reflection
Rfree0.2517 270 4.89 %
Rwork0.1987 --
obs0.2013 5518 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 63.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms519 0 19 17 555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096547
X-RAY DIFFRACTIONf_angle_d1.2321736
X-RAY DIFFRACTIONf_chiral_restr0.057572
X-RAY DIFFRACTIONf_plane_restr0.005895
X-RAY DIFFRACTIONf_dihedral_angle_d14.0054301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.650.32371290.26412551X-RAY DIFFRACTION100
2.65-39.790.23731410.18662697X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: -7.78124837802 Å / Origin y: 14.6094842513 Å / Origin z: -2.47862220803 Å
111213212223313233
T0.38389639745 Å20.0474823523186 Å2-0.0221110503579 Å2-0.345975521402 Å20.0196907004897 Å2--0.318792626612 Å2
L8.45860096883 °2-0.211247391185 °2-3.08663348628 °2-8.40789627105 °22.15108694945 °2--9.13709924504 °2
S-0.127378114201 Å °-0.480820093679 Å °-0.154655720058 Å °0.661709331743 Å °-0.0234985244083 Å °-0.300219150587 Å °0.639896962997 Å °0.296966974711 Å °0.167351543365 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 67)

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