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- PDB-1a6i: TET REPRESSOR, CLASS D VARIANT -

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Basic information

Entry
Database: PDB / ID: 1a6i
TitleTET REPRESSOR, CLASS D VARIANT
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION REGULATION / REPRESSOR / DNA-BINDING
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 D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOrth, P. / Cordes, F. / Schnappinger, D. / Hillen, W. / Saenger, W. / Hinrichs, W.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Conformational changes of the Tet repressor induced by tetracycline trapping.
Authors: Orth, P. / Cordes, F. / Schnappinger, D. / Hillen, W. / Saenger, W. / Hinrichs, W.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The Complex Formed between Tet Repressor and Tetracycline-Mg2+ Reveals Mechanism of Antibiotic Resistance
Authors: Kisker, C. / Hinrichs, W. / Tovar, K. / Hillen, W. / Saenger, W.
#2: Journal: Science / Year: 1994
Title: Structure of the Tet Repressor-Tetracycline Complex and Regulation of Antibiotic Resistance
Authors: Hinrichs, W. / Kisker, C. / Duvel, M. / Muller, A. / Tovar, K. / Hillen, W. / Saenger, W.
History
DepositionFeb 25, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D


Theoretical massNumber of molelcules
Total (without water)24,3201
Polymers24,3201
Non-polymers00
Water50428
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D

A: TETRACYCLINE REPRESSOR PROTEIN CLASS D


Theoretical massNumber of molelcules
Total (without water)48,6392
Polymers48,6392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area4440 Å2
ΔGint-44 kcal/mol
Surface area19490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.810, 69.810, 184.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein TETRACYCLINE REPRESSOR PROTEIN CLASS D / TET REPRESSOR / CLASS D


Mass: 24319.691 Da / Num. of mol.: 1
Mutation: A2S, N5D, R6K, E7S, S8K, D11N, A12S, T20V, D23E, I36V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 DELTA H1 DELTA TRP / Cellular location: CYTOPLASM / Plasmid: PWH610 (B/D)51-208 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACT4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.4 Å3/Da / Density % sol: 49 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Details: 0.01ml protein solution was mixed with 0.005ml reservoir
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2200 mM1dropNaCl
350 mMTris-HCl1drop
40.8 Mpotassium phosphate1reservoir
550 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→18.5 Å / Num. obs: 9076 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 42.4 Å2 / Rsym value: 0.073 / Net I/σ(I): 6.13
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.248 / % possible all: 98.6
Reflection
*PLUS
Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.248

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TCT

2tct


Resolution: 2.4→18.5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 909 10 %RANDOM
Rwork0.214 ---
obs0.214 9076 97.8 %-
Displacement parametersBiso mean: 47.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.4→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 0 28 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.92.5
X-RAY DIFFRACTIONx_mcangle_it2.293
X-RAY DIFFRACTIONx_scbond_it2.493
X-RAY DIFFRACTIONx_scangle_it2.93.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.PEP
X-RAY DIFFRACTION3TOPH19.SOL
X-RAY DIFFRACTION4TOPH19.HIS
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18

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