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- PDB-3a0j: Crystal structure of cold shock protein 1 from Thermus thermophil... -

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Basic information

Entry
Database: PDB / ID: 3a0j
TitleCrystal structure of cold shock protein 1 from Thermus thermophilus HB8
ComponentsCold shock proteinCold shock response
KeywordsTRANSCRIPTION / OB-fold / Cytoplasm / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


nucleic acid 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 domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold ...Cold shock, CspA / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / 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
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMiyazaki, T. / Nakagawa, N. / Kuramitsu, S. / Masui, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The Biological Action of Cold Shock Protein 1 from Thermus thermophilus HB8
Authors: Miyazaki, T. / Mega, R. / Kim, K. / Shikai, A. / Masui, R. / Kuramitsu, S. / Nakagawa, N.
History
DepositionMar 19, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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
B: Cold shock protein


Theoretical massNumber of molelcules
Total (without water)16,3942
Polymers16,3942
Non-polymers00
Water3,333185
1
A: Cold shock protein


Theoretical massNumber of molelcules
Total (without water)8,1971
Polymers8,1971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cold shock protein


Theoretical massNumber of molelcules
Total (without water)8,1971
Polymers8,1971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.215, 29.861, 38.264
Angle α, β, γ (deg.)67.37, 81.44, 79.49
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cold shock protein / Cold shock response


Mass: 8197.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0175 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLW8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.777856 Å3/Da / Density % sol: 30.815542 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 32% PEG 1500, 0.1M Tris HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 12948 / Num. obs: 12948 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 46.9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 13.9 / Num. unique all: 1166 / % possible all: 87.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HZA

1hza


Resolution: 1.65→21.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 306025.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1326 10.3 %RANDOM
Rwork0.165 ---
obs0.165 12817 94.3 %-
all-12948 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0224 Å2 / ksol: 0.410312 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å22.27 Å20.74 Å2
2--3.13 Å21.26 Å2
3----2.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.65→21.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 0 185 1343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.028
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d2.17
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.196 201 10 %
Rwork0.2 1809 -
obs-2010 88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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