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- PDB-2dg8: Crystal structure of the putative trasncriptional regulator SCO75... -

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Basic information

Entry
Database: PDB / ID: 2dg8
TitleCrystal structure of the putative trasncriptional regulator SCO7518 from Streptomyces coelicolor A3(2)
Componentsputative tetR-family transcriptional regulatory protein
KeywordsGENE REGULATION / helix-turn-helix motif / TetR family
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal, group 31 / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / TetR-family transcriptional regulatory protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.21 Å
AuthorsHayashi, T. / Watanabe, N. / Sakai, N. / Tamura, T. / Yao, M. / Tanaka, I.
CitationJournal: To be Published
Title: Crystal structure of the putative transcriptional regulator SCO7518 from Streptomyces coelicolor A3(2)
Authors: Hayashi, T. / Watanabe, N. / Tanaka, Y. / Sakai, N. / Tamura, T. / Yao, M. / Tanaka, I.
History
DepositionMar 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative tetR-family transcriptional regulatory protein
B: putative tetR-family transcriptional regulatory protein
C: putative tetR-family transcriptional regulatory protein
D: putative tetR-family transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)87,9314
Polymers87,9314
Non-polymers00
Water2,684149
1
A: putative tetR-family transcriptional regulatory protein
D: putative tetR-family transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)43,9652
Polymers43,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-16 kcal/mol
Surface area15210 Å2
MethodPISA
2
B: putative tetR-family transcriptional regulatory protein
C: putative tetR-family transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)43,9652
Polymers43,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-16 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.336, 101.262, 76.914
Angle α, β, γ (deg.)90.00, 98.60, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly of this protein is the dimer. The asymmetric unit of the crystal structure contains two dimer, PROA-PROD and PROB-PROC, respectively.

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Components

#1: Protein
putative tetR-family transcriptional regulatory protein


Mass: 21982.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Plasmid: pTip-QC2 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L-88 / References: GenBank: 14495028, UniProt: Q93J02*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 300mM diammonium hydrogen phosphate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 2.29 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.29 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 38773 / % possible obs: 99.7 % / Redundancy: 14 % / Biso Wilson estimate: 40.7 Å2 / Rsym value: 0.063
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 12.1 % / Num. unique all: 3825 / Rsym value: 0.298 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.21→19.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1516183.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1891 5 %RANDOM
Rwork0.218 ---
obs0.218 37953 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.5946 Å2 / ksol: 0.339346 e/Å3
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.15 Å20 Å2-1.02 Å2
2--14.18 Å20 Å2
3----6.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.21→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 0 0 149 5739
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.21→2.35 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 293 5.1 %
Rwork0.311 5487 -
obs--89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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