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- PDB-5xay: Crystal structure of full length tylp, a tetr regulator from stre... -

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Basic information

Entry
Database: PDB / ID: 5xay
TitleCrystal structure of full length tylp, a tetr regulator from streptomyces fradiae
ComponentsGamma-butyrolactone receptor protein
KeywordsDNA BINDING PROTEIN / TetR family / Transcription Regulator / Antibiotic Regulation / HTH DNA binding Domain
Function / homology
Function and homology information


regulation of gene expression / DNA binding
Similarity search - Function
DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Gamma-butyrolactone receptor protein TylP
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å
AuthorsRay, S. / Panjikar, S. / Anand, R.
Funding support Australia, India, 3items
OrganizationGrant numberCountry
Australia-India Council (AIC) grant Australia
DST IndiaEMR/2015/002121 India
BRNS India20150237B02RP00614-BRNS India
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Functional insights into the mode of DNA and ligand binding of the TetR family regulator TylP from Streptomyces fradiae
Authors: Ray, S. / Maitra, A. / Biswas, A. / Panjikar, S. / Mondal, J. / Anand, R.
History
DepositionMar 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-butyrolactone receptor protein
B: Gamma-butyrolactone receptor protein
C: Gamma-butyrolactone receptor protein
D: Gamma-butyrolactone receptor protein
E: Gamma-butyrolactone receptor protein
F: Gamma-butyrolactone receptor protein
G: Gamma-butyrolactone receptor protein
H: Gamma-butyrolactone receptor protein


Theoretical massNumber of molelcules
Total (without water)202,6908
Polymers202,6908
Non-polymers00
Water2,054114
1
A: Gamma-butyrolactone receptor protein
H: Gamma-butyrolactone receptor protein


Theoretical massNumber of molelcules
Total (without water)50,6722
Polymers50,6722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-26 kcal/mol
Surface area18830 Å2
MethodPISA
2
B: Gamma-butyrolactone receptor protein
F: Gamma-butyrolactone receptor protein


Theoretical massNumber of molelcules
Total (without water)50,6722
Polymers50,6722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-25 kcal/mol
Surface area19270 Å2
MethodPISA
3
C: Gamma-butyrolactone receptor protein
E: Gamma-butyrolactone receptor protein


Theoretical massNumber of molelcules
Total (without water)50,6722
Polymers50,6722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-24 kcal/mol
Surface area19570 Å2
MethodPISA
4
D: Gamma-butyrolactone receptor protein
G: Gamma-butyrolactone receptor protein


Theoretical massNumber of molelcules
Total (without water)50,6722
Polymers50,6722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-26 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.329, 71.885, 160.066
Angle α, β, γ (deg.)90.00, 102.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gamma-butyrolactone receptor protein / Gamma-butyrolactone receptor protein TylP


Mass: 25336.242 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Bacteria / Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: tylP, SFRA_26435 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9XCC7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.81 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Ammonium citrate tribasic (pH 7.0), 20% w/v PEG 3350
PH range: 5.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Type: OTHER / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.58→19.92 Å / Num. obs: 69940 / % possible obs: 99.5 % / Redundancy: 4.1 % / Net I/σ(I): 2.9
Reflection shellResolution: 2.58→2.62 Å / % possible obs: 98.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.621

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata processing
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.58→19.92 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.617 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28386 994 1.4 %RANDOM
Rwork0.22734 ---
obs0.22813 69922 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.667 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.58→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12723 0 0 114 12837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01912842
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.011.98917365
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92551623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61922.321573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.599152163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.29815162
X-RAY DIFFRACTIONr_chiral_restr0.1140.22091
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219470
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.58→2.646 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 53 -
Rwork0.326 4813 -
obs--98.36 %

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