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- PDB-1c9o: CRYSTAL STRUCTURE ANALYSIS OF THE BACILLUS CALDOLYTICUS COLD SHOC... -

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Basic information

Entry
Database: PDB / ID: 1c9o
TitleCRYSTAL STRUCTURE ANALYSIS OF THE BACILLUS CALDOLYTICUS COLD SHOCK PROTEIN BC-CSP
ComponentsCOLD-SHOCK PROTEIN
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 / AB INITIO / Resolution: 1.17 Å
AuthorsMueller, U. / Perl, D. / Schmid, F.X. / Heinemann, U.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein.
Authors: Mueller, U. / Perl, D. / Schmid, F.X. / Heinemann, U.
History
DepositionAug 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLD-SHOCK PROTEIN
B: COLD-SHOCK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0957
Polymers14,6822
Non-polymers4125
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.995, 76.995, 47.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Cell settingtetragonal
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-1078-

HOH

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Components

#1: Protein COLD-SHOCK PROTEIN / CSPB


Mass: 7341.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus caldolyticus (bacteria) / References: UniProt: P41016
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, HEPES, pH 7.5. VAPOR DIFFUSION, HANGING DROP at 293
Crystal
*PLUS
Density % sol: 2.05 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.6 mg/mlprotein1drop
210 mMTris-HCl1drop
3100 mMHEPES1reservoir
465 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9493
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9493 Å / Relative weight: 1
ReflectionResolution: 1.17→15 Å / Num. all: 45174 / Num. obs: 45174 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 33.4
Reflection shellResolution: 1.17→1.18 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.301 / % possible all: 38.8
Reflection
*PLUS
Lowest resolution: 15 Å
Reflection shell
*PLUS
% possible obs: 38.8 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.17→15 Å / Num. parameters: 1266 / Num. restraintsaints: 1481 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: USED RESTRAINED ANISOTROPIC DISPLACEMENT-FACTOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2307 5 %RANDOM, THIN RESOLUTION SHELLS
Rwork0.124 ---
all0.125 45174 --
obs0.124 45174 97 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 976 / Occupancy sum non hydrogen: 1321
Refinement stepCycle: LAST / Resolution: 1.17→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 26 274 1404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.02
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.1
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_plane_restr0.025
X-RAY DIFFRACTIONs_chiral_restr0.07

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