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- PDB-2dg6: Crystal structure of the putative transcriptional regulator SCO55... -

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Basic information

Entry
Database: PDB / ID: 2dg6
TitleCrystal structure of the putative transcriptional regulator SCO5550 from Streptomyces coelicolor A3(2)
Componentsputative transcriptional regulator
KeywordsGENE REGULATION / Winged-helix motif / MerR family
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
MerR family regulatory protein / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
: / Putative transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsHayashi, T. / Tanaka, Y. / Sakai, N. / Yao, M. / Tamura, T. / Tanaka, I.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2013
Title: Structural and genomic DNA analysis of a putative transcription factor SCO5550 from Streptomyces coelicolor A3(2): regulating the expression of gene sco5551 as a transcriptional activator with a novel dimer shape
Authors: Hayashi, T. / Tanaka, Y. / Sakai, N. / Watanabe, N. / Tamura, T. / Tanaka, I. / Yao, M.
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: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)25,2121
Polymers25,2121
Non-polymers00
Water1,69394
1
A: putative transcriptional regulator

A: putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)50,4242
Polymers50,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area8890 Å2
ΔGint-62 kcal/mol
Surface area17690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.689, 100.442, 38.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -x, -y+1, z.

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Components

#1: Protein putative transcriptional regulator


Mass: 25211.789 Da / Num. of mol.: 1
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: 3355698, UniProt: O86531*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.93 Å3/Da / Density % sol: 36.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Bis-Tris pH6.5, 1250mM Ammonium sulfate, 150mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9788, 0.9795, 0.900
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97951
30.91
ReflectionResolution: 2.1→50 Å / Num. obs: 11793 / % possible obs: 98.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.072
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.3 % / Num. unique all: 1041 / Rsym value: 0.224 / % possible all: 88.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.95 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1510278.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1008 9.7 %RANDOM
Rwork0.231 ---
obs0.231 10362 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.6542 Å2 / ksol: 0.389945 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--12.47 Å20 Å20 Å2
2---10.46 Å20 Å2
3---22.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1624 0 0 94 1718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
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_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 171 10.3 %
Rwork0.275 1483 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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