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- PDB-6szz: Crystal structure of Cold Shock Protein B (CspB) containing the m... -

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Basic information

Entry
Database: PDB / ID: 6szz
TitleCrystal structure of Cold Shock Protein B (CspB) containing the modified residue 4-F-Trp
ComponentsCold shock protein CspD
KeywordsSTRUCTURAL PROTEIN / fluorine cold shock domain
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 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 CspB / Cold shock protein CspB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)7,5743
Polymers7,3901
Non-polymers1842
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint0 kcal/mol
Surface area4650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.050, 56.050, 55.120
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 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: 7390.118 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 58.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS propane pH 7.0,1.2 M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→39.64 Å / Num. obs: 5913 / % possible obs: 99.8 % / Redundancy: 24.75 % / Biso Wilson estimate: 50.99 Å2 / CC1/2: 1 / Rsym value: 0.075 / Net I/σ(I): 28.89
Reflection shellResolution: 2.05→2.15 Å / Num. unique obs: 762 / CC1/2: 0.584 / Rsym value: 2.735

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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: 2.05→39.64 Å / SU ML: 0.2461 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.9561
RfactorNum. reflection% reflection
Rfree0.2312 306 5.2 %
Rwork0.2083 --
obs0.2097 5879 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms518 0 12 18 548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077538
X-RAY DIFFRACTIONf_angle_d0.9216719
X-RAY DIFFRACTIONf_chiral_restr0.049672
X-RAY DIFFRACTIONf_plane_restr0.004896
X-RAY DIFFRACTIONf_dihedral_angle_d13.5021306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.580.30361310.27752723X-RAY DIFFRACTION99.62
2.58-39.640.22271750.19622850X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.596043507 Å / Origin y: 7.78346539785 Å / Origin z: 11.6198798494 Å
111213212223313233
T0.377010031814 Å2-0.0315933112551 Å20.109619798831 Å2-0.38150403697 Å20.0532726482054 Å2--0.425244209097 Å2
L9.54906048378 °20.0100476034183 °21.96694878811 °2-8.73119497738 °21.99931257807 °2--8.94174857216 °2
S-0.133252229447 Å °-1.07173111564 Å °-0.450624267587 Å °0.701741666802 Å °-0.0672138493476 Å °0.236325813589 Å °0.572346831448 Å °-0.380191896832 Å °0.14803660164 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 67)

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