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- PDB-3oio: Crystal structure of transcriptional regulator (AraC-type DNA-bin... -

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Basic information

Entry
Database: PDB / ID: 3oio
TitleCrystal structure of transcriptional regulator (AraC-type DNA-binding domain-containing proteins) from Chromobacterium violaceum
ComponentsTranscriptional regulator (AraC-type DNA-binding domain-containing proteins)
KeywordsTRANSCRIPTION REGULATOR / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG / transcriptional regulator / DNA-binding
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Class I glutamine amidotransferase-like / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Class I glutamine amidotransferase-like / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator (AraC-type DNA-binding domain-containing proteins)
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsChang, C. / Mack, J. / Feldman, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of transcriptional regulator (AraC-type DNA-binding domain-containing proteins) from Chromobacterium violaceum
Authors: Chang, C. / Mack, J. / Feldman, B. / Joachimiak, A.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Dec 18, 2019Group: Database references / Derived calculations / Category: struct_conn / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator (AraC-type DNA-binding domain-containing proteins)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9723
Polymers12,8401
Non-polymers1322
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.753, 96.753, 33.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Transcriptional regulator (AraC-type DNA-binding domain-containing proteins)


Mass: 12840.261 Da / Num. of mol.: 1 / Fragment: sequence database residues 216-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: argR, CV_3088 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q7NTG7
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris propane, 1.5M Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, SITTING 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 315r / Detector: CCD / Date: Mar 8, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.65→31.67 Å / Num. all: 21726 / Num. obs: 21721 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 49.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 11 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 5 / Num. unique all: 1087 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→31.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.84 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 1997 9.3 %RANDOM
Rwork0.1608 ---
all0.1627 21452 --
obs0.1627 21452 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 113.72 Å2 / Biso mean: 25.2935 Å2 / Biso min: 6.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.65→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms891 0 6 106 1003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221105
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9691513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.885144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33822.67956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19315194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4521513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021893
X-RAY DIFFRACTIONr_mcbond_it1.7461.5671
X-RAY DIFFRACTIONr_mcangle_it3.12421099
X-RAY DIFFRACTIONr_scbond_it4.3623434
X-RAY DIFFRACTIONr_scangle_it7.0094.5414
X-RAY DIFFRACTIONr_rigid_bond_restr1.89831105
LS refinement shellResolution: 1.651→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 142 -
Rwork0.222 1382 -
all-1524 -
obs-1524 100 %
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)
10.3725-0.0747-0.04750.1992-0.1670.13920.01610.02550.00830.0096-0.0070.0043-0.0096-0.0069-0.0090.00910.0022-0.00020.0145-0.00330.000319.97145.115913.8048
20.2935-0.1729-0.07730.02340.02910.1655-0.0059-0.001-0.0285-0.0020.00120.01460.0059-0.00830.00470.00950.0008-0.0010.00840.00090.00927.057343.339326.9157
3-0.049-0.0467-0.00690.0584-0.01410.2705-0.0017-0.0065-0.0031-0.00080.0065-0.0038-0.0010.0051-0.00480.011800.00020.01040.0030.00355.040548.300834.2561
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A217 - 262
2X-RAY DIFFRACTION2A263 - 294
3X-RAY DIFFRACTION3A295 - 327

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