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- PDB-2qib: Crystal structure of tetR-family transcriptional regulator from S... -

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Basic information

Entry
Database: PDB / ID: 2qib
TitleCrystal structure of tetR-family transcriptional regulator from Streptomyces coelicolor
ComponentstetR-family transcriptional regulator
KeywordsTRANSCRIPTION / tetR-family transcriptional regulator / HTH DNA binding / Structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / 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
Putative tetR-family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of tetR-family transcriptional regulator from Streptomyces coelicolor.
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJul 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tetR-family transcriptional regulator
B: tetR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6166
Polymers51,4872
Non-polymers1,1294
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.607, 76.292, 65.262
Angle α, β, γ (deg.)90.00, 107.54, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein existed as dimer. The deposited MolA and MolB represent the dimer in the asymmetric unit.

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Components

#1: Protein tetR-family transcriptional regulator / HTH DNA binding domain


Mass: 25743.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Species: Streptomyces coelicolor / Strain: A3(2), M145 / Gene: GI:21220695, SCO2223, SC10B7.18 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9KZ14
#2: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M KH2PO4, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→62.6 Å / Num. all: 53412 / Num. obs: 52953 / % possible obs: 99.14 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 24.64
Reflection shellResolution: 1.7→1.743 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 1.79 / Num. unique all: 3754 / % possible all: 91.05

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→62.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.44 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.103
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21412 2832 5.1 %RANDOM
Rwork0.17733 ---
all0.17921 52953 --
obs0.17921 52953 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0.39 Å2
2--0.32 Å20 Å2
3----1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.043 Å0.038 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 1.7→62.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 75 619 4042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223482
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9964696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2325426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07922.222162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05515555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7861543
X-RAY DIFFRACTIONr_chiral_restr0.0870.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022623
X-RAY DIFFRACTIONr_nbd_refined0.210.21921
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22449
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2483
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.241
X-RAY DIFFRACTIONr_mcbond_it0.9621.52193
X-RAY DIFFRACTIONr_mcangle_it1.56323423
X-RAY DIFFRACTIONr_scbond_it2.88531423
X-RAY DIFFRACTIONr_scangle_it4.2554.51273
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 214 -
Rwork0.26 3540 -
obs-3754 91.05 %
Refinement TLS params.Method: refined / Origin x: 0.067 Å / Origin y: 8.293 Å / Origin z: 9.544 Å
111213212223313233
T-0.0316 Å20.0127 Å2-0.0037 Å2--0.0085 Å2-0.0114 Å2---0.0623 Å2
L0.1455 °2-0.024 °20.1193 °2-0.3539 °20.1735 °2--0.5509 °2
S0.0309 Å °-0.0707 Å °0.021 Å °-0.0127 Å °-0.0632 Å °0.0402 Å °0.0172 Å °-0.0358 Å °0.0323 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 200
5X-RAY DIFFRACTION1A201 - 230
6X-RAY DIFFRACTION1B14 - 60
7X-RAY DIFFRACTION1B61 - 120
8X-RAY DIFFRACTION1B121 - 170
9X-RAY DIFFRACTION1B171 - 228
10X-RAY DIFFRACTION1A701 - 703
11X-RAY DIFFRACTION1A705 - 986

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