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Basic information

Entry
Database: PDB / ID: 2gen
TitleStructural Genomics, the crystal structure of a probable transcriptional regulator from Pseudomonas aeruginosa PAO1
Componentsprobable transcriptional regulator
KeywordsTRANSCRIPTION / APC6095 / Pseudomonas aeruginosa PA01 / TetR family / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
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. / Homeobox-like domain superfamily ...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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsTan, K. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a probable transcriptional regulator from Pseudomonas aeruginosa PAO1
Authors: Tan, K. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMar 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE MOLECULE CAN EXIST IN BOTH MONOMERIC AND DIMERIC FORMS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE DIMERIC FORM.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)21,8271
Polymers21,8271
Non-polymers00
Water3,153175
1
A: probable transcriptional regulator

A: probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,6542
Polymers43,6542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)38.335, 69.130, 176.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-196-

HOH

21A-305-

HOH

DetailsThe biological assembly is a dimer. In the crystal structure, there is one monomer in one asymmetric unit. The other pairing monomer can be generated by a symmetry operation of (-X+1,-Y,Z).

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Components

#1: Protein probable transcriptional regulator


Mass: 21827.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Gene: 15597033 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9I2Q9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.2M di-Ammonium Tartrate, 0.1M NaAcetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Mar 7, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.7→18.03 Å / Num. all: 26394 / Num. obs: 26275 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Biso Wilson estimate: 27.52 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 43.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.45 / Num. unique all: 2588 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→18.03 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.038 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24842 1333 5.1 %RANDOM
Rwork0.20967 ---
all0.21164 24914 --
obs0.21164 24914 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.167 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 0 175 1642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211497
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.9272025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2815187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69221.68877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61215236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0271520
X-RAY DIFFRACTIONr_chiral_restr0.1340.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021169
X-RAY DIFFRACTIONr_nbd_refined0.2110.2706
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.216
X-RAY DIFFRACTIONr_mcbond_it1.0891.5954
X-RAY DIFFRACTIONr_mcangle_it1.68421459
X-RAY DIFFRACTIONr_scbond_it2.7113621
X-RAY DIFFRACTIONr_scangle_it3.8884.5566
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 84 -
Rwork0.285 1808 -
obs--99.47 %

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