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- PDB-6wpa: Structure of AvaR1 bound to DNA half-site -

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Basic information

Entry
Database: PDB / ID: 6wpa
TitleStructure of AvaR1 bound to DNA half-site
Components
  • AvaR1
  • PAL2-1-5'-GC
KeywordsDNA BINDING PROTEIN/DNA / Transcriptional Repressor / DNA oligonucleotide / DNA-Protein biniding / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / : / 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
DNA / DNA (> 10) / Gamma-butyrolactone receptor protein
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsKapoor, I. / Olivares, P.J. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2020
Title: Biochemical basis for the regulation of biosynthesis of antiparasitics by bacterial hormones.
Authors: Kapoor, I. / Olivares, P. / Nair, S.K.
History
DepositionApr 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: AvaR1
B: AvaR1
M: PAL2-1-5'-GC
N: PAL2-1-5'-GC
C: AvaR1
D: AvaR1
E: AvaR1
F: AvaR1
G: AvaR1
H: AvaR1


Theoretical massNumber of molelcules
Total (without water)233,51010
Polymers233,51010
Non-polymers00
Water00
1
A: AvaR1
M: PAL2-1-5'-GC
D: AvaR1
E: AvaR1
H: AvaR1

A: AvaR1
M: PAL2-1-5'-GC
D: AvaR1
E: AvaR1
H: AvaR1


Theoretical massNumber of molelcules
Total (without water)233,51010
Polymers233,51010
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area24990 Å2
ΔGint-131 kcal/mol
Surface area77030 Å2
MethodPISA
2
B: AvaR1
N: PAL2-1-5'-GC
F: AvaR1

B: AvaR1
N: PAL2-1-5'-GC
F: AvaR1

C: AvaR1
G: AvaR1

C: AvaR1
G: AvaR1


Theoretical massNumber of molelcules
Total (without water)233,51010
Polymers233,51010
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-y,x,z-1/21
crystal symmetry operation4_554y,-x,z-1/21
Buried area24730 Å2
ΔGint-132 kcal/mol
Surface area76420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.522, 130.522, 180.649
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
AvaR1 / Putative gamma-butyrolactone receptor protein


Mass: 27037.654 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: AvaR1 bound to DNA oligonucleotide through its DNA binding domain
Source: (gene. exp.) Streptomyces avermitilis (bacteria)
Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680
Gene: avaR1, SAVERM_3705 / Plasmid: Rosetta
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q82H41
#2: DNA chain PAL2-1-5'-GC


Mass: 8604.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Palindromic double stranded DNA (28-MER)
Source: (synth.) Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)

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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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Potassium chloride, 0.01 M Magnesium chloride hexahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.5, 10% w/v Polyethylene glycol 4000 with additive 40 % Formamide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.08→25 Å / Num. obs: 55544 / % possible obs: 100 % / Redundancy: 15.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.021 / Rrim(I) all: 0.079 / Net I/σ(I): 25.9
Reflection shellResolution: 3.09→3.2 Å / Num. unique obs: 5510 / CC1/2: 0.999 / Rpim(I) all: 0.338

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WP7

6wp7


Resolution: 3.09→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.645 / SU ML: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 2787 5 %RANDOM
Rwork0.2104 ---
obs0.2131 52651 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 213.84 Å2 / Biso mean: 106.635 Å2 / Biso min: 48.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0 Å2-0 Å2
2--1.08 Å2-0 Å2
3----2.15 Å2
Refinement stepCycle: final / Resolution: 3.09→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13178 1148 0 0 14326
Num. residues----1752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01914688
X-RAY DIFFRACTIONr_angle_refined_deg1.361.89320120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58651688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28822.997614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.922152327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.26815139
X-RAY DIFFRACTIONr_chiral_restr0.0930.22260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110687
LS refinement shellResolution: 3.09→3.165 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.386 176 -
Rwork0.331 3844 -
obs--99.95 %

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