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- PDB-2dg7: Crystal structure of the putative transcriptional regulator SCO03... -

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Basic information

Entry
Database: PDB / ID: 2dg7
TitleCrystal structure of the putative transcriptional regulator SCO0337 from Streptomyces coelicolor A3(2)
Componentsputative transcriptional regulator
KeywordsGENE REGULATION / helix-turn-helix motif / TetR family
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
MftR, C-terminal / MftR C-terminal domain / : / Tetracycline Repressor, domain 2 / 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
: / Transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsHayashi, T. / Tanaka, Y. / Sakai, N. / Yao, M. / Tamura, T. / Tanaka, I.
CitationJournal: To be Published
Title: Crystal structure of the putative transcriptional regulator SCO0337 from Streptomyces coelicolor A3(2)
Authors: Hayashi, T. / Tanaka, Y. / Sakai, N. / Yao, M. / Tamura, T. / 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: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)21,4431
Polymers21,4431
Non-polymers00
Water99155
1
A: putative transcriptional regulator

A: putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)42,8852
Polymers42,8852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2440 Å2
ΔGint-17 kcal/mol
Surface area18480 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.952, 42.864, 43.933
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+1, -y+1, z.

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Components

#1: Protein putative transcriptional regulator


Mass: 21442.734 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: 5912516, UniProt: Q9RK42*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES pH7.0, 9% Jeffamine ED-2001 reagent pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97934, 0.97950, 0.98338
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.97951
30.983381
ReflectionResolution: 2.3→50 Å / Num. obs: 9138 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.049
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.4 % / Num. unique all: 872 / Rsym value: 0.204 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→9.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1105378.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 879 9.8 %RANDOM
Rwork0.23 ---
obs0.23 8970 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.8184 Å2 / ksol: 0.553281 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2--7.95 Å20 Å2
3----6.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→9.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 0 55 1481
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
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_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.59
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.722.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 164 11.3 %
Rwork0.22 1285 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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