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

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Basic information

Entry
Database: PDB / ID: 1hzc
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 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
Similarity search - Component
Biological speciesBacillus caldolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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
DepositionJan 24, 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)14,5653
Polymers14,5422
Non-polymers231
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.864, 76.864, 48.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 7271.027 Da / Num. of mol.: 2 / Mutation: R3E,E46A,L66E
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


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, cacodylate, pH 6.5, 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
354 %MPD1reservoir
4100 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8428 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 2000 / Details: crystal
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8428 Å / Relative weight: 1
ReflectionResolution: 1.32→20 Å / Num. all: 32636 / Num. obs: 32636 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 37.8
Reflection shellResolution: 1.32→1.33 Å / Redundancy: 2 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 1 / Num. unique all: 796 / % possible all: 97.7
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 97.7 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C9O

1c9o


Resolution: 1.32→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Shelxl-97 (Sheldrick) was also used for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.181 3298 -thin shells 10%
Rwork0.139 ---
all0.144 32610 --
obs0.144 32610 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.32→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 1 270 1368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d2.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.5

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