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- PDB-3d3o: Crystal structure of the effector domain of the putative transcri... -

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Basic information

Entry
Database: PDB / ID: 3d3o
TitleCrystal structure of the effector domain of the putative transcriptional regulator IclR from Acinetobacter sp. ADP1
ComponentsPutative transcriptional regulator, IcIR familyTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / alpha-beta structure / effector domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Putative transcriptional regulator (IcIR family)
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å
AuthorsKim, Y. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Effector Domain of the Putative Transcriptional Regulator IclR from Acinetobacter sp. ADP1.
Authors: Kim, Y. / Shackelford, G. / Joachimiak, A.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transcriptional regulator, IcIR family
B: Putative transcriptional regulator, IcIR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5468
Polymers41,0482
Non-polymers4986
Water1,874104
1
A: Putative transcriptional regulator, IcIR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7163
Polymers20,5241
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative transcriptional regulator, IcIR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8305
Polymers20,5241
Non-polymers3064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.382, 71.681, 96.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Putative transcriptional regulator, IcIR family / Transcriptional regulation


Mass: 20524.051 Da / Num. of mol.: 2 / Fragment: Effector domain: Residues 81-255
Source method: isolated from a genetically manipulated source
Details: N-term 6-His-tag with TEV protease cleavage site / Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Gene: ACIAD1822 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FBA6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 1.26M Ammonium sulfate, 0.1M CHES pH 9.5, 0.2M NaCl, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2008 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.46→35.84 Å / Num. all: 15652 / Num. obs: 15652 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 53.69 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 9 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.3 / Num. unique all: 778 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.46→35.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.897 / SU B: 19.088 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.499 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.269 780 5 %RANDOM
Rwork0.195 ---
all0.198 14818 --
obs0.198 14818 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.159 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.46→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 26 104 2874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222927
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9613970
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5215370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.1624.414145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.04815542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1271525
X-RAY DIFFRACTIONr_chiral_restr0.1120.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022220
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.21379
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22041
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2156
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9861.51847
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59922917
X-RAY DIFFRACTIONr_scbond_it2.38631195
X-RAY DIFFRACTIONr_scangle_it3.4624.51053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 53 -
Rwork0.298 1075 -
obs-1128 98.52 %
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)
14.1406-1.1305-1.20243.6367-0.15232.3983-0.1143-0.66860.04560.2680.1214-0.10570.0650.3368-0.0071-0.2629-0.0014-0.0544-0.2207-0.0284-0.348833.273436.179775.5819
26.41980.51450.78863.0355-1.63783.86240.10381.021310.0729-0.07010.0492-0.30440.0907-0.0337-0.2570.0810.0658-0.09520.168-0.088526.691449.779141.7982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 1721 - 175
2X-RAY DIFFRACTION2BB-2 - 1691 - 172

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