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- PDB-2i5m: Crystal structure of Bacillus subtilis cold shock protein CspB va... -

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Basic information

Entry
Database: PDB / ID: 2i5m
TitleCrystal structure of Bacillus subtilis cold shock protein CspB variant A46K S48R
ComponentsCold shock protein cspBCold shock response
KeywordsGENE REGULATION / oligonucleotide/oligosaccharide binding fold / cold shock domain / beta-barrel / DNA binding protein / expression regulator
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMax, K.E.A. / Heinemann, U.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Optimized variants of the cold shock protein from in vitro selection: structural basis of their high thermostability.
Authors: Max, K.E. / Wunderlich, M. / Roske, Y. / Schmid, F.X. / Heinemann, U.
History
DepositionAug 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Cold shock protein cspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5252
Polymers7,5001
Non-polymers241
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
X: Cold shock protein cspB
hetero molecules

X: Cold shock protein cspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0494
Polymers15,0012
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_646y+1,x-1,-z+11
Buried area1270 Å2
ΔGint-33 kcal/mol
Surface area8320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.627, 58.627, 46.798
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cold shock protein cspB / Cold shock response / Major cold shock protein


Mass: 7500.345 Da / Num. of mol.: 1 / Mutation: A46K, S48R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: cspB, cspA / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P32081
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.09 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: reservoir solution: 1.5 M lithium sulfate, 0.1 M TRIS pH 7.5, 15% glycerol for cryoprotection. protein solution: 20 mM TRIS pH 7.5, 50 mM NaCl, 3 mM MgCl2, 17.4 mg/ml protein. ...Details: reservoir solution: 1.5 M lithium sulfate, 0.1 M TRIS pH 7.5, 15% glycerol for cryoprotection. protein solution: 20 mM TRIS pH 7.5, 50 mM NaCl, 3 mM MgCl2, 17.4 mg/ml protein. crystallization setup: 0.8 microliter protein solution:0.8 microliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9537 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 18, 2005 / Details: mirrors
RadiationMonochromator: double-crystal monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.22→20 Å / Num. all: 4700 / Num. obs: 4621 / % possible obs: 98.319 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 41.593 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 26.65
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 7.9 / Num. measured obs: 2087 / Num. unique all: 390 / % possible all: 83.3

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Phasing

Phasing MRRfactor: 0.419 / Cor.coef. Fo:Fc: 0.598 / Cor.coef. Io to Ic: 0.577
Highest resolutionLowest resolution
Rotation3 Å8 Å
Translation3 Å8 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345v. 0.9.31data collection
XDSVERSION June 2005data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1CSP

1csp


Resolution: 2.3→19.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.41 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic + TLS refinement / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.262 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 214 5 %RANDOM
Rwork0.204 ---
obs0.205 4231 98.624 %-
all-4290 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.462 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å21.04 Å20 Å2
2--2.08 Å20 Å2
3----3.12 Å2
Refine analyzeLuzzati coordinate error free: 0.197 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms521 0 1 23 545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021540
X-RAY DIFFRACTIONr_bond_other_d0.0040.02466
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.921722
X-RAY DIFFRACTIONr_angle_other_deg2.01831094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.867565
X-RAY DIFFRACTIONr_chiral_restr0.0750.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02615
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02114
X-RAY DIFFRACTIONr_nbd_refined0.1580.263
X-RAY DIFFRACTIONr_nbd_other0.1870.2495
X-RAY DIFFRACTIONr_nbtor_other0.0830.2335
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0610.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.22
X-RAY DIFFRACTIONr_mcbond_it0.5822322
X-RAY DIFFRACTIONr_mcangle_it1.0663514
X-RAY DIFFRACTIONr_scbond_it1.4834.5218
X-RAY DIFFRACTIONr_scangle_it2.3866208
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 15 -
Rwork0.244 288 -
obs-303 97.1 %
Refinement TLS params.Method: refined / Origin x: 36.644 Å / Origin y: -24.9506 Å / Origin z: 12.3127 Å
111213212223313233
T0.1454 Å20.0897 Å20.0141 Å2-0.0659 Å2-0.0325 Å2--0.1615 Å2
L5.0602 °2-0.9044 °20.9051 °2-5.0971 °2-2.6991 °2--11.3731 °2
S0.1392 Å °0.2668 Å °-0.1636 Å °-0.6985 Å °-0.0766 Å °-0.1114 Å °0.5213 Å °0.0672 Å °-0.0625 Å °
Refinement TLS groupSelection: ALL

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