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- PDB-1y0u: Crystal Structure of the putative arsenical resistance operon rep... -

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Basic information

Entry
Database: PDB / ID: 1y0u
TitleCrystal Structure of the putative arsenical resistance operon repressor from Archaeoglobus fulgidus
Componentsarsenical resistance operon repressor, putative
KeywordsTRANSCRIPTION REPRESSOR / Structural Genomics / Protein Structure Initiative / PSI / Midwest Center For Structural Genomocs / MCSG / Arsenical Resistance Operon Repressor / HTH_ARSR / DNA-binding protein / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Helix-turn-helix 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
ACETATE ION / Arsenical resistance operon repressor, putative
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKim, Y. / Joachimiak, A. / Skarina, T. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the putative arsenical resistance operon repressor from Archaeoglobus fulgidus
Authors: Kim, Y. / Joachimiak, A. / Skarina, T. / Savchenko, A. / Edwards, A.
History
DepositionNov 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 26, 2012Group: Structure summary
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: arsenical resistance operon repressor, putative
B: arsenical resistance operon repressor, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7123
Polymers22,6532
Non-polymers591
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-17 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.741, 43.244, 61.674
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein arsenical resistance operon repressor, putative


Mass: 11326.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O30069
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 36.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 3350, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97916 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 21, 2004 / Details: mirrors
RadiationMonochromator: double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.6→61.31 Å / Num. all: 25483 / Num. obs: 22399 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1156 / % possible all: 45.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→61.31 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.539 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20144 1123 5.1 %RANDOM
Rwork0.17172 ---
all0.17331 20973 --
obs0.17331 20973 86.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.174 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20.76 Å2
2---0.74 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→61.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 4 263 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221630
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.9672207
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2535214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26822.96381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81215354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1441518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021214
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2793
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21105
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9581.5968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28121528
X-RAY DIFFRACTIONr_scbond_it2.2993755
X-RAY DIFFRACTIONr_scangle_it3.5344.5659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 38 -
Rwork0.229 713 -
obs-713 40.79 %

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