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- PDB-5mru: TetR(class A) in complex with 5a,6-anhydrotetracycline and magnesium -

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Basic information

Entry
Database: PDB / ID: 5mru
TitleTetR(class A) in complex with 5a,6-anhydrotetracycline and magnesium
ComponentsTetracycline Repressor, class A
KeywordsTRANSCRIPTION / Repressor / Tetracycline / helix-turn-helix
Function / homology
Function and homology information


response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, 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 ...Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, 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
5A,6-ANHYDROTETRACYCLINE / Tetracycline repressor protein class A from transposon 1721
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHinrichs, W. / Palm, G.J.
Citation
Journal: To Be Published
Title: TetR(class A) in complex with 5a,6-anhydrotetracycline and magnesium
Authors: Hinrichs, W. / Palm, G.J.
#1: Journal: FEBS Journal / Year: 2016
Title: Modular Organisation of Inducer Recognition and Allostery in the Tetracycline Repressor
Authors: Werten, S. / Schneider, J. / Palm, G.J. / Hinrichs, W.
History
DepositionDec 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetracycline Repressor, class A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7663
Polymers23,3151
Non-polymers4512
Water1629
1
A: Tetracycline Repressor, class A
hetero molecules

A: Tetracycline Repressor, class A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5326
Polymers46,6302
Non-polymers9014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3200 Å2
ΔGint-35 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.669, 65.669, 98.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Tetracycline Repressor, class A


Mass: 23315.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P03038*PLUS
#2: Chemical ChemComp-TDC / 5A,6-ANHYDROTETRACYCLINE


Mass: 426.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N2O7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2uL complex [10uL TetR(A) with 39.6 mg/ml TetR(A) + 50uL anTC (2mM in 200mM NaCl) + 0.25uL MgCl2 (3M) + 40uL H2O] + Reservoir 1uL (0.026mM (NH4)H2HPO4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 1, 2008 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.505→54.65 Å / Num. obs: 7877 / % possible obs: 98.2 % / Observed criterion σ(I): -1 / Redundancy: 4.8 % / Biso Wilson estimate: 56.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Net I/σ(I): 12.37
Reflection shellResolution: 2.505→2.66 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.02 / CC1/2: 0.444 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSNovember 3, 2014data reduction
XDSNovember 3, 2014data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vpr

2vpr


Resolution: 2.55→54.65 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 29.357 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.576 / ESU R Free: 0.319 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27132 733 9.9 %RANDOM
Rwork0.22806 ---
obs0.23241 6658 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.846 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å2-0 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.55→54.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 32 9 1305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191317
X-RAY DIFFRACTIONr_bond_other_d0.0010.021219
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9841796
X-RAY DIFFRACTIONr_angle_other_deg0.8832763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09523.15857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12315185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1731512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02309
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6192.736689
X-RAY DIFFRACTIONr_mcbond_other1.6192.736688
X-RAY DIFFRACTIONr_mcangle_it2.6034.092856
X-RAY DIFFRACTIONr_mcangle_other2.6014.092857
X-RAY DIFFRACTIONr_scbond_it1.572.806627
X-RAY DIFFRACTIONr_scbond_other1.5622.807621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5914.164931
X-RAY DIFFRACTIONr_long_range_B_refined4.54222.3281634
X-RAY DIFFRACTIONr_long_range_B_other4.44622.2661613
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 45 -
Rwork0.359 450 -
obs--92.87 %
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)
16.14612.29794.061411.07744.14787.0421-0.4327-0.41450.71930.21210.23890.3019-1.1222-0.30940.19380.3120.05210.00250.0946-0.02570.12378.094828.17976.4894
27.04320.81612.1468.0635-0.91283.13480.08-1.2061-0.61890.62030.1931.39770.2289-0.6519-0.2730.1342-0.08670.06910.35660.22520.3904-3.42749.66155.0538
39.04383.8914-8.183817.6712-15.137520.15450.08770.08-0.6885-0.3236-0.10250.67370.9670.05240.01480.2544-0.1439-0.12890.36020.00990.4191-6.17770.7861-3.5657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 36
2X-RAY DIFFRACTION1A37 - 39
3X-RAY DIFFRACTION1A40 - 64
4X-RAY DIFFRACTION2A65 - 156
5X-RAY DIFFRACTION2A222 - 1011
6X-RAY DIFFRACTION3A178 - 208

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