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- PDB-3cdl: Crystal structure of a TetR family transcriptional regulator from... -

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Basic information

Entry
Database: PDB / ID: 3cdl
TitleCrystal structure of a TetR family transcriptional regulator from Pseudomonas syringae pv. tomato str. DC3000
ComponentsTranscriptional regulator AefR
KeywordsTRANSCRIPTION REGULATOR / APC88582 / TetR / Pseudomonas syringae pv. tomato str. DC3000 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


Transcriptional regulator TetR, C-terminal, Proteobacteria type / AefR-like transcriptional repressor, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...Transcriptional regulator TetR, C-terminal, Proteobacteria type / AefR-like transcriptional repressor, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator AefR
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.36 Å
AuthorsTan, K. / Bigelow, L. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a TetR family transcriptional regulator from Pseudomonas syringae pv. tomato str. DC3000.
Authors: Tan, K. / Bigelow, L. / Gu, M. / Joachimiak, A.
History
DepositionFeb 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 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: Transcriptional regulator AefR
B: Transcriptional regulator AefR


Theoretical massNumber of molelcules
Total (without water)46,8662
Polymers46,8662
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-34.4 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.305, 53.409, 55.829
Angle α, β, γ (deg.)90.00, 113.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional regulator AefR


Mass: 23432.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: aefR, PSPTO3549 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87Z81
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.93 Å3/Da / Density % sol: 36.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium acetate, 25% PEG 3350, 0.1M Bis-Tris, pH 5.5, 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: 0.97915, 0.97937
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979371
ReflectionResolution: 2.35→33.26 Å / Num. all: 14467 / Num. obs: 14467 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 15.47
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 1025 / % possible all: 80.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.36→33.26 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.907 / SU B: 26.49 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.729 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27514 728 5 %RANDOM
Rwork0.20667 ---
all0.21037 13723 --
obs0.21037 13723 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.514 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.16 Å2
2--0.17 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.36→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 0 41 3063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223096
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9424194
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26623.377151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.44215529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9931527
X-RAY DIFFRACTIONr_chiral_restr0.1170.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022349
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.21513
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22125
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.661.51916
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06223008
X-RAY DIFFRACTIONr_scbond_it1.4931360
X-RAY DIFFRACTIONr_scangle_it2.3114.51185
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.36→2.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 53 -
Rwork0.264 795 -
obs-848 76.95 %
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)
16.2147-2.7221-4.52655.88721.17857.5259-0.85410.1458-1.56830.0584-0.05430.68311.5234-0.16490.90840.2321-0.06440.1682-0.1541-0.10410.265866.785-0.172-36.426
21.5070.5151-1.30210.6388-0.81034.2513-0.03970.0137-0.23310.0007-0.0931-0.01690.2871-0.0260.1328-0.20580.0274-0.0693-0.21-0.0223-0.101659.51514.9-13.403
35.5585-0.7388-0.53393.9098-1.06949.24920.55870.82020.808-0.1172-0.1367-0.1908-0.8724-0.6242-0.42190.18070.21290.09080.20170.14320.070658.76532.204-46.166
42.132-0.1884-0.72521.26870.18574.39340.19470.09450.44670.05530.035-0.0111-0.649-0.0332-0.2297-0.12470.0501-0.0262-0.20950.0078-0.023355.84531.554-19.145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 656 - 68
2X-RAY DIFFRACTION2AA70 - 19973 - 202
3X-RAY DIFFRACTION3BB3 - 646 - 67
4X-RAY DIFFRACTION4BB73 - 20076 - 203

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