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- PDB-2hyj: The crystal structure of a tetR-family transcriptional regulator ... -

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Basic information

Entry
Database: PDB / ID: 2hyj
TitleThe crystal structure of a tetR-family transcriptional regulator from Streptomyces coelicolor
ComponentsPutative tetR-family transcriptional regulator
KeywordsTRANSCRIPTION / tetR / HTH DNA binding motif / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA binding / metal ion binding
Similarity search - Function
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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative tetR-family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2006
Title: The crystal structure of a tetR-family transcriptional regulator from Streptomyces coelicolor
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,9033
Polymers21,7671
Non-polymers1362
Water2,288127
1
A: Putative tetR-family transcriptional regulator
hetero molecules

A: Putative tetR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8066
Polymers43,5332
Non-polymers2724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3810 Å2
ΔGint-63 kcal/mol
Surface area16590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)32.864, 82.678, 178.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-214-

HOH

31A-313-

HOH

DetailsThis protein exists as dimer. The second part of the biological assembly is generated by the two fold axis: 1-x, 1-y,z

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Components

#1: Protein Putative tetR-family transcriptional regulator


Mass: 21766.691 Da / Num. of mol.: 1 / Fragment: HTH DNA binding motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: GI:32141251 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8CJS4
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na Hepes, 0.2M Calcium chloride, 28% PEG400, pH 7.5, 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: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.19→89.4 Å / Num. all: 12463 / Num. obs: 12388 / % possible obs: 99.43 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 18.04
Reflection shellResolution: 2.19→2.25 Å / Redundancy: 7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / Num. unique all: 924 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.19→44.7 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.673 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.222 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 635 4.9 %RANDOM
Rwork0.1913 ---
obs0.1939 12388 99.43 %-
all-12463 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.136 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---0.34 Å20 Å2
3----0.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.042 Å0.035 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.19→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 6 127 1607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211501
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9692031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9725192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13822.67671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56115251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1171519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021148
X-RAY DIFFRACTIONr_nbd_refined0.2160.2722
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2107
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4790.22
X-RAY DIFFRACTIONr_mcbond_it0.7171.5986
X-RAY DIFFRACTIONr_mcangle_it1.21921509
X-RAY DIFFRACTIONr_scbond_it2.3513578
X-RAY DIFFRACTIONr_scangle_it3.8364.5522
LS refinement shellResolution: 2.19→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 34 -
Rwork0.21 824 -
obs-858 92.86 %
Refinement TLS params.Method: refined / Origin x: 13.043 Å / Origin y: 29.706 Å / Origin z: 30.002 Å
111213212223313233
T-0.1146 Å2-0.0102 Å20.0107 Å2--0.0966 Å20.0107 Å2---0.1208 Å2
L0.6923 °20.0857 °2-0.0582 °2-1.8241 °20.1885 °2--2.7763 °2
S0.0523 Å °0.1832 Å °0.0588 Å °0.1456 Å °-0.0702 Å °0.0001 Å °0.308 Å °-0.0421 Å °0.0179 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 509 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 150101 - 150
4X-RAY DIFFRACTION1AA151 - 200151 - 200

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