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- PDB-3iuv: The structure of a member of TetR family (SCO1917) from Streptomy... -

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Basic information

Entry
Database: PDB / ID: 3iuv
TitleThe structure of a member of TetR family (SCO1917) from Streptomyces coelicolor A3
Componentsuncharacterized TetR family protein
Keywordsstructural genomics / unknown function / APC6223 / TetR / Streptomyces coelicolor A3 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
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 ...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
HTH tetR-type domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.554 Å
AuthorsTan, K. / Cuff, M. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a member of TetR family (SCO1917) from Streptomyces coelicolor A3
Authors: Tan, K. / Cuff, M. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized TetR family protein


Theoretical massNumber of molelcules
Total (without water)21,5281
Polymers21,5281
Non-polymers00
Water00
1
A: uncharacterized TetR family protein

A: uncharacterized TetR family protein


Theoretical massNumber of molelcules
Total (without water)43,0562
Polymers43,0562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area2650 Å2
ΔGint-19 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.577, 58.577, 109.226
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsauthors state that the biological unit is experimentally unknown. According to crystal contact, the chain A and its symmetry-related molecule (X-Y, -Y, -Z+2/3) form a dimer.

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Components

#1: Protein uncharacterized TetR family protein


Mass: 21528.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: A3 / Gene: SCI7.35c, SCO1917, Streptomyces coelicolor / Plasmid: p15Tv lic / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9X9V5

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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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.1M Na(CAc), 3.5M Naformate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948, 0.97959
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2007 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979481
20.979591
ReflectionResolution: 2.55→46 Å / Num. all: 7324 / Num. obs: 7324 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 59.6
Reflection shellResolution: 2.55→2.61 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.7 / Num. unique all: 401 / % possible all: 85.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.554→46 Å / SU ML: 0.48 / σ(F): 1.34 / σ(I): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2882 340 4.65 %random
Rwork0.2407 ---
obs0.2431 7315 98.08 %-
all-7315 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.218 Å2 / ksol: 0.37 e/Å3
Refinement stepCycle: LAST / Resolution: 2.554→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 0 0 1259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091279
X-RAY DIFFRACTIONf_angle_d1.3481750
X-RAY DIFFRACTIONf_dihedral_angle_d20.518443
X-RAY DIFFRACTIONf_chiral_restr0.079212
X-RAY DIFFRACTIONf_plane_restr0.006231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5538-3.21750.33141630.27163377X-RAY DIFFRACTION97
3.2175-46.01650.27841770.23383598X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9333-0.9717-0.32860.3399-0.40991.3333-0.4962-1.10990.1957-0.0253-0.0708-0.23280.0139-0.03880.51320.5144-0.08230.10721.0586-0.04950.742117.158736.969626.8419
22.5858-0.3266-1.38341.67030.73292.9710.1436-0.4376-0.2142-0.1020.2002-0.2730.55950.6414-0.2710.57720.07550.01360.7295-0.02120.6637-8.03143.003530.5486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 7:50A7 - 50
2X-RAY DIFFRACTION2chain A and resid 51:179A51 - 179

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