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- PDB-3f6o: Crystal structure of ArsR family transcriptional regulator, RHA00566 -

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Basic information

Entry
Database: PDB / ID: 3f6o
TitleCrystal structure of ArsR family transcriptional regulator, RHA00566
ComponentsProbable transcriptional regulator, ArsR family protein
Keywordstranscription regulator / ArsR family / transcriptional regulator / RHA00566 / MCSG / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Helix-turn-helix domain / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Probable transcriptional regulator, ArsR family protein
Similarity search - Component
Biological speciesRhodococcus sp. RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsDong, A. / Xu, X. / Zheng, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of ArsR family transcriptional regulator, RHA00566
Authors: Dong, A. / Xu, X. / Zheng, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A.
History
DepositionNov 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transcriptional regulator, ArsR family protein
B: Probable transcriptional regulator, ArsR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1925
Polymers26,9532
Non-polymers2403
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-17 kcal/mol
Surface area10650 Å2
MethodPISA
2
A: Probable transcriptional regulator, ArsR family protein
hetero molecules

A: Probable transcriptional regulator, ArsR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2726
Polymers26,9532
Non-polymers3204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1470 Å2
ΔGint-8 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.543, 65.543, 93.024
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-122-

HOH

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Components

#1: Protein Probable transcriptional regulator, ArsR family protein


Mass: 13476.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. RHA1 (bacteria) / Gene: RHA1_ro06925 / Plasmid: PET DERIVATIVE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)DERIVATIVE / References: UniProt: Q0S195
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE PROTEIN WAS CRYSTALLIZED BY IN SITU PTOTEOLYSIS METHOD, THE PROTEIN WAS ...AUTHORS STATE THAT THE PROTEIN WAS CRYSTALLIZED BY IN SITU PTOTEOLYSIS METHOD, THE PROTEIN WAS MIXED WITH 200:1(W/W) WITH THERMOLYSIN. THE FULL SEQUENCE WENT INTO CRYSTALLIZATION TRIAL IS MGSSHHHHHHSSGRENLYFQGMAQYPEQLNGIFQALADPTRRAVLGRLSRGPATVSELA KPFDMALPSFMKHIHFLEDSGWIRTHKQGRVRTCAIEKEPFTAVEAWLAEQQELWESRTDRL EQFVTEHTVTAHAKATPQ

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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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-tris pH5.5 0.2M MgCl2 25%PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 297K
PH range: pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9199 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 18153 / Num. obs: 18153 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1726 / Rsym value: 0.428 / % possible all: 93.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.2.0019refinement
Coot0.3.3model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.475 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24693 592 3.2 %RANDOM
Rwork0.21595 ---
all0.21692 18153 --
obs0.21692 17965 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.591 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.24 Å20 Å2
2--0.47 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 3 159 1646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9382064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6485186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47523.09971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98615250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7841513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021167
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2707
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21053
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9951.5965
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67121503
X-RAY DIFFRACTIONr_scbond_it2.5013638
X-RAY DIFFRACTIONr_scangle_it4.154.5561
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 51 -
Rwork0.283 1207 -
obs--91.82 %

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