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- PDB-2g7s: The crystal structure of transcriptional regulator, TetR family, ... -

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Basic information

Entry
Database: PDB / ID: 2g7s
TitleThe crystal structure of transcriptional regulator, TetR family, from Agrobacterium tumefaciens
Componentstranscriptional regulator, TetR family
KeywordsTRANSCRIPTION / APC5906 / TetR / PSI / Protein structure initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


regulation of biosynthetic process / regulation of primary metabolic process / DNA binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / 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
: / Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsLunin, V.V. / Chang, C. / Xu, X. / Gu, J. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of transcriptional regulator, TetR family, from Agrobacterium tumefaciens
Authors: Lunin, V.V. / Chang, C. / Xu, X. / Gu, J. / Joachimiak, A. / Edwards, A.M. / Savchenko, A.
History
DepositionFeb 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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, TetR family


Theoretical massNumber of molelcules
Total (without water)21,3351
Polymers21,3351
Non-polymers00
Water5,783321
1
A: transcriptional regulator, TetR family

A: transcriptional regulator, TetR family


Theoretical massNumber of molelcules
Total (without water)42,6702
Polymers42,6702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2870 Å2
ΔGint-22 kcal/mol
Surface area16070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.736, 55.029, 73.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

DetailsBiological assembly is a dimer, formed by a molecule from the asymmetric unit plus (-x, -y, z) symmetry-related molecule

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Components

#1: Protein transcriptional regulator, TetR family


Mass: 21334.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 17738610, UniProt: A9CKG4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5M K3PO4,0.5M Na3PO4 , pH 7.5, 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: 0.9793164 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793164 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 38903 / Num. obs: 38903 / % possible obs: 99.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 6.9 % / Rsym value: 0.085 / Net I/σ(I): 35
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.506 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.779 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18605 1951 5 %RANDOM
Rwork0.13648 ---
obs0.13896 36936 99.67 %-
all-36936 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.502 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 0 321 1777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211687
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9372313
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5095226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14622.20877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54215281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.791518
X-RAY DIFFRACTIONr_chiral_restr0.1480.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021335
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.2907
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21229
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3981.51085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.29221730
X-RAY DIFFRACTIONr_scbond_it4.4133667
X-RAY DIFFRACTIONr_scangle_it5.8164.5583
X-RAY DIFFRACTIONr_rigid_bond_restr2.72431752
X-RAY DIFFRACTIONr_sphericity_free10.7273322
X-RAY DIFFRACTIONr_sphericity_bonded6.39531638
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 131 -
Rwork0.177 2588 -
obs--96.93 %

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