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- PDB-2ns7: How an in vitro selected peptide mimics the antibiotic tetracycli... -

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Basic information

Entry
Database: PDB / ID: 2ns7
TitleHow an in vitro selected peptide mimics the antibiotic tetracycline to induce TET repressor
ComponentsTetracycline repressor protein
KeywordsTRANSCRIPTION / transcription regulator / helix-turn-helix
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / 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
Tetracycline repressor protein class B from transposon Tn10 / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLuckner, S.R. / Klotzsche, M. / Berens, C. / Hillen, W. / Muller, Y.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: How an agonist peptide mimics the antibiotic tetracycline to induce Tet-repressor
Authors: Luckner, S.R. / Klotzsche, M. / Berens, C. / Hillen, W. / Muller, Y.A.
History
DepositionNov 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetracycline repressor protein
B: Tetracycline repressor protein
C: Tetracycline repressor protein
D: Tetracycline repressor protein


Theoretical massNumber of molelcules
Total (without water)94,1274
Polymers94,1274
Non-polymers00
Water00
1
A: Tetracycline repressor protein
B: Tetracycline repressor protein


Theoretical massNumber of molelcules
Total (without water)47,0632
Polymers47,0632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-36 kcal/mol
Surface area19660 Å2
MethodPISA
2
C: Tetracycline repressor protein
D: Tetracycline repressor protein


Theoretical massNumber of molelcules
Total (without water)47,0632
Polymers47,0632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-28 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.910, 107.910, 303.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALARGARGAA9 - 1049 - 104
21VALVALARGARGBB9 - 1049 - 104
31VALVALARGARGCC9 - 1049 - 104
41VALVALARGARGDD9 - 1049 - 104
52LEULEUVALVALAA120 - 153120 - 153
62LEULEUVALVALBB120 - 153120 - 153
72LEULEUVALVALCC120 - 153120 - 153
82LEULEUVALVALDD120 - 153120 - 153
93ALAALATHRTHRAA182 - 202182 - 202
103ALAALATHRTHRBB182 - 202182 - 202
113ALAALATHRTHRCC182 - 202182 - 202
123ALAALATHRTHRDD182 - 202182 - 202

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Components

#1: Protein
Tetracycline repressor protein


Mass: 23531.662 Da / Num. of mol.: 4 / Mutation: C68S, C88N, C121T, C144S
Source method: isolated from a genetically manipulated source
Details: residues 1-187 are from VARIANT B, residues 188-208 are from VARIANT D
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tetR / Plasmid: pWH610 / Production host: Escherichia coli (E. coli) / Strain (production host): RB791 / References: UniProt: P04483, UniProt: P0ACT4

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M ammonium sulfate, 0.1M sodium chloride, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.946452 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 22, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946452 Å / Relative weight: 1
ReflectionResolution: 2.4→37.04 Å / Num. obs: 41266 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.819 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 28.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.4-2.450.4724.918606239698
2.45-2.620.4087.184977689098.1
2.62-2.80.26911.184919561098.3
2.8-30.18315.472302480298.4
3-3.40.09825.498300655698.5
3.4-3.90.05341.972951491498.6
3.9-4.80.05357.795861453998.9
4.80.05160.974295342298.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345softwaredata collection
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NS8 (Chain A+B)

2ns8


Resolution: 2.4→37.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 22.295 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: individual isotropic and TLS refinement
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3302 8 %RANDOM
Rwork0.23 ---
obs0.234 41265 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.794 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å21.67 Å20 Å2
2--3.34 Å20 Å2
3----5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 0 0 0 6027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216144
X-RAY DIFFRACTIONr_bond_other_d0.0010.025593
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9578304
X-RAY DIFFRACTIONr_angle_other_deg0.805313014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6145750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99524.575306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.937151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4491536
X-RAY DIFFRACTIONr_chiral_restr0.0650.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021213
X-RAY DIFFRACTIONr_nbd_refined0.2060.21531
X-RAY DIFFRACTIONr_nbd_other0.1580.25285
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23018
X-RAY DIFFRACTIONr_nbtor_other0.0860.23499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.25
X-RAY DIFFRACTIONr_mcbond_it0.6411.54903
X-RAY DIFFRACTIONr_mcbond_other0.0821.51550
X-RAY DIFFRACTIONr_mcangle_it0.74825997
X-RAY DIFFRACTIONr_scbond_it1.07932712
X-RAY DIFFRACTIONr_scangle_it1.6154.52307
Refine LS restraints NCS

Ens-ID: 1 / Number: 2311 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.865
2BLOOSE POSITIONAL0.755
3CLOOSE POSITIONAL0.715
4DLOOSE POSITIONAL0.855
1ALOOSE THERMAL1.7410
2BLOOSE THERMAL1.7710
3CLOOSE THERMAL1.8210
4DLOOSE THERMAL1.6210
LS refinement shellResolution: 2.4→2.484 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.344 313 -
Rwork0.266 3591 -
obs-3904 100 %
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)
11.7589-0.91890.15973.48643.7226.4484-0.2319-0.26320.23470.36060.2535-0.31040.12280.1219-0.0215-0.33840.03140.0245-0.2687-0.0711-0.09119.674743.060327.0137
23.05060.7484-3.58450.55070.18827.31670.2221-0.233-0.0002-0.01390.10630.24150.36510.0063-0.3284-0.25280.09860.0663-0.24390.0552-0.094-2.394228.056428.982
32.16931.3701-1.58991.4282-3.268810.27690.1190.15970.2247-0.12290.1956-0.18080.63450.71-0.31460.19370.13460.0113-0.08570.1294-0.1267-23.868115.869826.5219
42.9251-1.02554.35711.2484-2.06229.18950.3548-0.2253-0.1118-0.22710.07860.33380.5456-0.745-0.43350.0634-0.0689-0.1447-0.20030.1853-0.0503-44.360813.191328.3936
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 1546 - 154
21AA165 - 202165 - 202
32BB6 - 1546 - 154
42BB165 - 202165 - 202
53CC7 - 1547 - 154
63CC165 - 202165 - 202
74DD6 - 1546 - 154
84DD182 - 202182 - 202

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