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- PDB-1i5f: BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMI... -

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Basic information

Entry
Database: PDB / ID: 1i5f
TitleBACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY
ComponentsCOLD-SHOCK PROTEIN CSPB
KeywordsTRANSCRIPTION / Beta barrel / Homodimer
Function / homology
Function and homology information


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 caldolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDelbrueck, H. / Mueller, U. / Perl, D. / Schmid, F.X. / Heinemann, U.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structures of mutant forms of the Bacillus caldolyticus cold shock protein differing in thermal stability.
Authors: Delbruck, H. / Mueller, U. / Perl, D. / Schmid, F.X. / Heinemann, U.
History
DepositionFeb 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.4Aug 9, 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
A: COLD-SHOCK PROTEIN CSPB
B: COLD-SHOCK PROTEIN CSPB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6493
Polymers14,6262
Non-polymers231
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.120, 77.120, 48.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-1006-

HOH

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Components

#1: Protein COLD-SHOCK PROTEIN CSPB / CSPB / BC-CSP


Mass: 7313.107 Da / Num. of mol.: 2 / Mutation: R3E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus caldolyticus (bacteria) / Gene: CSPB / Production host: Escherichia coli (E. coli) / References: UniProt: P41016
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 6000, sodium citrate, ammonia sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
210 mMsodium-HEPES1drop
330 %PEG60001reservoir
4100 mMsodium citrate1reservoir
5200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9493 / Wavelength: 0.9493 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9493 Å / Relative weight: 1
ReflectionResolution: 1.4→15 Å / Num. all: 26730 / Num. obs: 26715 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 18.9
Reflection shellResolution: 1.4→1.41 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.6 / Num. unique all: 380 / % possible all: 91.8
Reflection
*PLUS
% possible obs: 96 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 92.6 % / Rmerge(I) obs: 0.329

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C9O

1c9o


Resolution: 1.4→15 Å / Num. parameters: 12045 / Num. restraintsaints: 14073 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.205 130 4 %RANDOM
Rwork0.139 ---
all0.14 26715 --
obs0.139 26730 95.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 964 / Occupancy sum non hydrogen: 1256
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 1 253 1337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.07
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Num. reflection Rfree: 1306 / % reflection Rfree: 5 % / Rfactor all: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg0.023

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