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- PDB-2ns8: How an in vitro selected peptide mimics the antibiotic tetracycli... -

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Basic information

Entry
Database: PDB / ID: 2ns8
TitleHow an in vitro selected peptide mimics the antibiotic tetracycline to induce TET repressor
Components
  • 16 residue peptide Tip (Transcription inducing peptide)
  • Tetracycline repressor protein
KeywordsTRANSCRIPTION / Transcription regulator / helix-turn-helix / bound repressor-inducing peptide
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.4Aug 23, 2017Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.5Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetracycline repressor protein
B: Tetracycline repressor protein
C: Tetracycline repressor protein
D: Tetracycline repressor protein
H: 16 residue peptide Tip (Transcription inducing peptide)
E: 16 residue peptide Tip (Transcription inducing peptide)
F: 16 residue peptide Tip (Transcription inducing peptide)
G: 16 residue peptide Tip (Transcription inducing peptide)
Z: 16 residue peptide Tip (Transcription inducing peptide)


Theoretical massNumber of molelcules
Total (without water)102,4709
Polymers102,4709
Non-polymers00
Water00
1
A: Tetracycline repressor protein
B: Tetracycline repressor protein
H: 16 residue peptide Tip (Transcription inducing peptide)
E: 16 residue peptide Tip (Transcription inducing peptide)
Z: 16 residue peptide Tip (Transcription inducing peptide)


Theoretical massNumber of molelcules
Total (without water)52,0705
Polymers52,0705
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-73 kcal/mol
Surface area18590 Å2
MethodPISA
2
C: Tetracycline repressor protein
D: Tetracycline repressor protein
F: 16 residue peptide Tip (Transcription inducing peptide)
G: 16 residue peptide Tip (Transcription inducing peptide)


Theoretical massNumber of molelcules
Total (without water)50,4014
Polymers50,4014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-69 kcal/mol
Surface area17990 Å2
MethodPISA
3
C: Tetracycline repressor protein
D: Tetracycline repressor protein
F: 16 residue peptide Tip (Transcription inducing peptide)
G: 16 residue peptide Tip (Transcription inducing peptide)

A: Tetracycline repressor protein
B: Tetracycline repressor protein
H: 16 residue peptide Tip (Transcription inducing peptide)
E: 16 residue peptide Tip (Transcription inducing peptide)
Z: 16 residue peptide Tip (Transcription inducing peptide)


Theoretical massNumber of molelcules
Total (without water)102,4709
Polymers102,4709
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_555-x+1/2,y+1/2,-z1
identity operation1_555x,y,z1
Buried area22380 Å2
ΔGint-150 kcal/mol
Surface area35170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.890, 200.590, 65.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
12H
22E
32F
42G

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSSERSERAA8 - 688 - 68
211LYSLYSSERSERBB8 - 688 - 68
311LYSLYSSERSERCC8 - 688 - 68
411LYSLYSSERSERDD8 - 688 - 68
521SERSERALAALAAA74 - 15474 - 154
621SERSERALAALABB74 - 15474 - 154
721SERSERALAALACC74 - 15474 - 154
821SERSERALAALADD74 - 15474 - 154
931METMETGLNGLNAA166 - 200166 - 200
1031METMETGLNGLNBB166 - 200166 - 200
1131METMETGLNGLNCC166 - 200166 - 200
1231METMETGLNGLNDD166 - 200166 - 200
112TRPTRPALAALAHE1 - 102 - 11
212TRPTRPALAALAEF1 - 102 - 11
312TRPTRPALAALAFG1 - 102 - 11
412TRPTRPALAALAGH1 - 102 - 11

NCS ensembles :
ID
1
2

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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
#2: Protein/peptide
16 residue peptide Tip (Transcription inducing peptide)


Mass: 1668.764 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: peptide has been synthesized / Source: (synth.) synthetic construct (others)
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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 4M sodium formate, 0.1M Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 13, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 33932 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.938 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.55-2.710.4833.726231531698.2
2.71-2.890.3365.325159507799.6
2.89-3.120.2377.323388473099.7
3.12-3.420.13511.821648438499.7
3.42-3.820.0771919524396999.7
3.82-4.40.05125.817332356599.7
4.4-5.370.04728.114691302999.8
5.370.04727.111401240199.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TCT

2tct


Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 24.42 / SU ML: 0.246 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: individual isotropic and TLS refinement
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.74 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2713 8 %RANDOM
Rwork0.206 ---
obs0.211 33914 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: 46.989 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---3.15 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6884 0 0 0 6884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217038
X-RAY DIFFRACTIONr_bond_other_d0.0010.026321
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9499537
X-RAY DIFFRACTIONr_angle_other_deg0.841314695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.72424.423355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.243151199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8241542
X-RAY DIFFRACTIONr_chiral_restr0.0740.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021423
X-RAY DIFFRACTIONr_nbd_refined0.2340.21856
X-RAY DIFFRACTIONr_nbd_other0.1740.26604
X-RAY DIFFRACTIONr_nbtor_refined0.1870.23498
X-RAY DIFFRACTIONr_nbtor_other0.0910.24144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.24
X-RAY DIFFRACTIONr_mcbond_it0.6911.55468
X-RAY DIFFRACTIONr_mcbond_other0.1011.51743
X-RAY DIFFRACTIONr_mcangle_it0.82426830
X-RAY DIFFRACTIONr_scbond_it1.25233172
X-RAY DIFFRACTIONr_scangle_it1.914.52707
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2727LOOSE POSITIONAL0.815
12B2727LOOSE POSITIONAL0.885
13C2727LOOSE POSITIONAL0.85
14D2727LOOSE POSITIONAL0.785
11A2727LOOSE THERMAL1.8810
12B2727LOOSE THERMAL2.8910
13C2727LOOSE THERMAL2.1610
14D2727LOOSE THERMAL1.7210
21H153LOOSE POSITIONAL0.35
22E153LOOSE POSITIONAL0.655
23F153LOOSE POSITIONAL0.335
24G153LOOSE POSITIONAL0.295
21H153LOOSE THERMAL3.7310
22E153LOOSE THERMAL1.0710
23F153LOOSE THERMAL2.1710
24G153LOOSE THERMAL1.310
LS refinement shellResolution: 2.553→2.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.351 382 -
Rwork0.279 4389 -
obs-4771 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)
11.2374-0.39210.34243.1938-0.11140.97750.04260.10660.225-0.24290.00520.0051-0.0312-0.0258-0.0478-0.2754-0.0079-0.0102-0.1945-0.0106-0.322129.239154.080114.9233
22.25350.89120.27171.0962-0.00130.62980.01650.1634-0.0744-0.26950.0429-0.23190.01540.1753-0.0595-0.23720.0135-0.0004-0.15450.0197-0.300946.501246.527218.7681
30.94720.75910.49355.06962.29051.062-0.0646-0.0861-0.13340.5187-0.14850.28590.06140.02370.2131-0.13380.00470.0395-0.1622-0.0122-0.096515.7139.1618-7.8827
41.42821.2846-0.16625.14-1.71850.6857-0.16040.2174-0.2972-0.3463-0.0866-0.43410.08890.22360.247-0.1420.05380.079-0.1071-0.0389-0.063126.82767.218-23.3339
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
31HE1 - 102 - 11
42BB6 - 1546 - 154
52BB165 - 202165 - 202
62EF1 - 102 - 11
73CC6 - 1546 - 154
83CC165 - 202165 - 202
93FG1 - 102 - 11
104DD6 - 1546 - 154
114DD165 - 202165 - 202
124GH1 - 102 - 11

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