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- PDB-5xaz: Crystal structure of full length native tylp, a tetr regulator fr... -

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Basic information

Entry
Database: PDB / ID: 5xaz
TitleCrystal structure of full length native 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 DNA-templated transcription / DNA binding
Similarity search - Function
: / : / Tetracyclin repressor-like, C-terminal domain / 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: 2.3 Å
AuthorsRay, S. / Panjikar, S. / Anand, R.
Funding support Australia, India, 3items
OrganizationGrant numberCountry
Australia-India Council (AIC) grant Australia
DST, Govt. of 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: Database references / Category: citation
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
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
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-butyrolactone receptor protein
H: 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


Theoretical massNumber of molelcules
Total (without water)200,1258
Polymers200,1258
Non-polymers00
Water8,269459
1
A: Gamma-butyrolactone receptor protein
H: Gamma-butyrolactone receptor protein


Theoretical massNumber of molelcules
Total (without water)50,0312
Polymers50,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-27 kcal/mol
Surface area19940 Å2
MethodPISA
2
B: Gamma-butyrolactone receptor protein
C: Gamma-butyrolactone receptor protein


Theoretical massNumber of molelcules
Total (without water)50,0312
Polymers50,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-28 kcal/mol
Surface area20030 Å2
MethodPISA
3
D: Gamma-butyrolactone receptor protein
E: Gamma-butyrolactone receptor protein


Theoretical massNumber of molelcules
Total (without water)50,0312
Polymers50,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-27 kcal/mol
Surface area20130 Å2
MethodPISA
4
F: Gamma-butyrolactone receptor protein
G: Gamma-butyrolactone receptor protein


Theoretical massNumber of molelcules
Total (without water)50,0312
Polymers50,0312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-28 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.479, 71.566, 158.584
Angle α, β, γ (deg.)90.00, 102.92, 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: 25015.652 Da / Num. of mol.: 8 / Mutation: R113A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: tylP, SFRA_26435 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9XCC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.95 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 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.3→19.81 Å / Num. obs: 98807 / % possible obs: 99.7 % / Redundancy: 3.5 % / Net I/σ(I): 2.8
Reflection shellResolution: 2.3→2.42 Å / % possible obs: 96.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.481

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata processing
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.57 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.22 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25258 992 1 %RANDOM
Rwork0.20401 ---
obs0.20451 97167 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.099 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13339 0 0 459 13798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01913541
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.97818337
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90851729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80222.31606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.369152356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.52315174
X-RAY DIFFRACTIONr_chiral_restr0.1410.22185
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110110
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: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 72 -
Rwork0.303 6482 -
obs--94.85 %

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