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- PDB-3f6v: Crystal structure of Possible transcriptional regulator for arsen... -

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Basic information

Entry
Database: PDB / ID: 3f6v
TitleCrystal structure of Possible transcriptional regulator for arsenical resistance
ComponentsPossible transcriptional regulator, ArsR family protein
Keywordstranscription regulator / Rhodococcus sp. / probable transcriptional repressor ArsR family / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
: / Bacterial regulatory protein, arsR family / 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 ...: / Bacterial regulatory protein, arsR family / 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
Possible transcriptional regulator, ArsR family protein
Similarity search - Component
Biological speciesRhodococcus sp. RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsChang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Possible transcriptional regulator for arsenical resistance from Rhodococcus sp.
Authors: Chang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, 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 1.2Sep 3, 2014Group: Refinement description
Revision 1.3Dec 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,0182
Polymers16,9941
Non-polymers241
Water2,342130
1
A: Possible transcriptional regulator, ArsR family protein
hetero molecules

A: Possible transcriptional regulator, ArsR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0374
Polymers33,9882
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3070 Å2
ΔGint-31 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.106, 42.106, 104.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Possible transcriptional regulator, ArsR family protein


Mass: 16994.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. RHA1 (bacteria) / Gene: RHA1_ro04124 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q0S966
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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

Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.2M Mg(OAC), 20%PEG3350, 1/200 papain w/w, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2008
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 16477 / Num. obs: 16305 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 26.4 % / Biso Wilson estimate: 18.518 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 83.18
Reflection shellResolution: 1.48→1.49 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 8.57 / Num. unique all: 294 / % possible all: 73.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→39.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.465 / SU ML: 0.044 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19929 806 5 %RANDOM
Rwork0.15943 ---
all0.16143 16084 --
obs0.16143 15278 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.48→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 0 1 130 893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022867
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9651194
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.725119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.422.29248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34315155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.231514
X-RAY DIFFRACTIONr_chiral_restr0.1090.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021692
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_it1.7111.5524
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5842854
X-RAY DIFFRACTIONr_scbond_it3.5093343
X-RAY DIFFRACTIONr_scangle_it5.0294.5329
X-RAY DIFFRACTIONr_rigid_bond_restr2.0343867
X-RAY DIFFRACTIONr_sphericity_free8.1623131
X-RAY DIFFRACTIONr_sphericity_bonded5.673841
LS refinement shellResolution: 1.482→1.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 69 -
Rwork0.158 1073 -
obs-1142 96.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1062-0.0638-0.44710.9025-0.27052.36340.02320.0241-0.013-0.0516-0.03990.03440.0043-0.14440.01680.0274-0.0179-0.0130.03280.00750.0077-1.0482.86417.458
21.27490.3578-0.1780.2718-0.30071.75390.08290.06580.098-0.06440.05520.0221-0.0431-0.288-0.13820.06820.0130.02350.05010.02850.023-4.5547.9949.302
30.8466-0.18061.28561.0261-0.54922.1284-0.03970.11220.01810.00590.00760.0666-0.13060.15960.03210.0527-0.0013-0.00650.01640.00570.01485.4210.6256.497
40.128-0.1923-0.02220.5821-0.31160.47140.0141-0.0216-0.0316-0.0456-0.04620.0095-0.00990.04670.0320.01290.0096-0.00080.04820.02060.01435.199-6.46232.442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 48
2X-RAY DIFFRACTION2A49 - 78
3X-RAY DIFFRACTION3A79 - 97
4X-RAY DIFFRACTION4A98 - 121

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