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- PDB-3e7q: The crystal structure of the putative transcriptional regulator f... -

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Basic information

Entry
Database: PDB / ID: 3e7q
TitleThe crystal structure of the putative transcriptional regulator from Pseudomonas aeruginosa PAO1
Componentstranscriptional regulator
Keywordstranscription regulator / transcriptional regulator / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the putative transcriptional regulator from Pseudomonas aeruginosa PAO1
Authors: Zhang, R. / Skarine, T. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: transcriptional regulator
B: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)46,8892
Polymers46,8892
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-26 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.613, 53.706, 57.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThis protein exists as dimer. The deposited Mol A/B represents the dimer in the asymmetric unit.

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Components

#1: Protein transcriptional regulator


Mass: 23444.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4984 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HUI1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG3350, 0.2M MgNitrate, NDSB 256, 0.3M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2.2→80.32 Å / Num. all: 24450 / Num. obs: 23472 / % possible obs: 0.96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.7 / Net I/σ(I): 35
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1880 / % possible all: 0.767

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→80.32 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.625 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.282 / ESU R Free: 0.233
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26551 1259 5.1 %RANDOM
Rwork0.21389 ---
obs0.21674 23472 96 %-
all-24450 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.457 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--0.65 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.2→80.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 0 133 3339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213277
X-RAY DIFFRACTIONr_bond_other_d0.0020.022232
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9494439
X-RAY DIFFRACTIONr_angle_other_deg1.13235364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0725416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88722.468154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70715517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8081534
X-RAY DIFFRACTIONr_chiral_restr0.10.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02736
X-RAY DIFFRACTIONr_nbd_refined0.230.2877
X-RAY DIFFRACTIONr_nbd_other0.2030.22246
X-RAY DIFFRACTIONr_nbtor_refined0.180.21607
X-RAY DIFFRACTIONr_nbtor_other0.0950.21677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3390.216
X-RAY DIFFRACTIONr_mcbond_it1.2161.52280
X-RAY DIFFRACTIONr_mcbond_other0.2311.5864
X-RAY DIFFRACTIONr_mcangle_it1.74523237
X-RAY DIFFRACTIONr_scbond_it2.61731352
X-RAY DIFFRACTIONr_scangle_it3.8224.51202
LS refinement shellResolution: 2.204→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 81 -
Rwork0.258 1361 -
obs-1442 76.7 %
Refinement TLS params.Method: refined / Origin x: 24.609 Å / Origin y: -8.095 Å / Origin z: 51.958 Å
111213212223313233
T-0.1172 Å20.0118 Å2-0.0206 Å2--0.0922 Å20.0153 Å2---0.0412 Å2
L1.4892 °20.9166 °2-0.2573 °2-1.1773 °2-0.1675 °2--0.7546 °2
S0.0081 Å °0.0978 Å °0.2191 Å °-0.0422 Å °0.0006 Å °0.1968 Å °-0.0527 Å °-0.051 Å °-0.0088 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 502 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 150101 - 150
4X-RAY DIFFRACTION1AA151 - 209151 - 209
5X-RAY DIFFRACTION1BB1 - 501 - 50
6X-RAY DIFFRACTION1BB51 - 10051 - 100
7X-RAY DIFFRACTION1BB101 - 150101 - 150
8X-RAY DIFFRACTION1BB151 - 210151 - 210

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