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- PDB-4v2f: Tetracycline repressor TetR(D), unliganded -

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Basic information

Entry
Database: PDB / ID: 4v2f
TitleTetracycline repressor TetR(D), unliganded
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / REPRESSOR / ANTIBIOTIC RESISTANCE / TETR
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 / DNA-binding HTH domain, TetR-type ...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
AuthorsWerten, S. / Orth, P. / Saenger, W. / Hinrichs, W.
CitationJournal: Biochemistry / Year: 2014
Title: Tetracycline Repressor Allostery Does not Depend on Divalent Metal Recognition.
Authors: Werten, S. / Dalm, D. / Palm, G.J. / Grimm, C.C. / Hinrichs, W.
History
DepositionOct 9, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionDec 10, 2014ID: 1BJ0
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)23,2881
Polymers23,2881
Non-polymers00
Water0
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D

A: TETRACYCLINE REPRESSOR PROTEIN CLASS D


Theoretical massNumber of molelcules
Total (without water)46,5772
Polymers46,5772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area4520 Å2
ΔGint-37 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.790, 69.790, 182.340
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


Mass: 23288.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWH208 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: 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: 2.38 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 8 / Details: PH 8.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9995
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9995 Å / Relative weight: 1
ReflectionResolution: 2.4→30.8 Å / Num. obs: 7162 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.3 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TCT

2tct


Resolution: 2.4→65.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.991 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.674 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27811 796 10 %RANDOM
Rwork0.2076 ---
obs0.21495 7162 86.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.762 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2--1.91 Å20 Å2
3----3.82 Å2
Refinement stepCycle: LAST / Resolution: 2.4→65.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 0 0 1541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191567
X-RAY DIFFRACTIONr_bond_other_d0.0010.021525
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9672118
X-RAY DIFFRACTIONr_angle_other_deg0.81233485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82223.54479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.55115278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5411515
X-RAY DIFFRACTIONr_chiral_restr0.080.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
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_it5.316.738770
X-RAY DIFFRACTIONr_mcbond_other5.36.738769
X-RAY DIFFRACTIONr_mcangle_it7.8810.094959
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4197.358797
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 48 -
Rwork0.303 542 -
obs--90.77 %

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