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- PDB-1bjz: TETRACYCLINE CHELATED MG2+-ION INITIATES HELIX UNWINDING FOR TET ... -

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Basic information

Entry
Database: PDB / ID: 1bjz
TitleTETRACYCLINE CHELATED MG2+-ION INITIATES HELIX UNWINDING FOR TET REPRESSOR INDUCTION
ComponentsTETRACYCLINE REPRESSOR
KeywordsTRANSCRIPTION REGULATION / DNA-BINDING PROTEIN / HTH-MOTIF
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: 2.2 Å
AuthorsOrth, P. / Saenger, W. / Hinrichs, W.
Citation
Journal: Biochemistry / Year: 1999
Title: Tetracycline-chelated Mg2+ ion initiates helix unwinding in Tet repressor induction.
Authors: Orth, P. / Saenger, W. / Hinrichs, W.
#1: 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.
History
DepositionJun 29, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 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


Theoretical massNumber of molelcules
Total (without water)23,2881
Polymers23,2881
Non-polymers00
Water48627
1
A: TETRACYCLINE REPRESSOR

A: TETRACYCLINE REPRESSOR


Theoretical massNumber of molelcules
Total (without water)46,5772
Polymers46,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area4640 Å2
ΔGint-38 kcal/mol
Surface area19630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.100, 69.100, 182.930
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 / TET REPRESSOR / CLASS D


Mass: 23288.334 Da / Num. of mol.: 1 / Mutation: A2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0ACT4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.34 Å3/Da / Density % sol: 40 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.4 mMTetR(D)1drop
2200 mM1dropNaCl
310 mMTris-HCl1drop
41 Mammonium sulfate1reservoir
5200 mM1reservoirNaCl
620 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→23.6 Å / Num. obs: 32245 / % possible obs: 89 % / Redundancy: 3.1 % / Biso Wilson estimate: 47.3 Å2 / Rsym value: 0.083 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.36 / % possible all: 93.1
Reflection
*PLUS
Num. obs: 10487 / % possible obs: 89.5 % / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Lowest resolution: 2.3 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3.8

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Processing

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

2tct


Resolution: 2.2→23.6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1024 8.7 %RANDOM
Rwork0.232 ---
obs0.232 10487 89.5 %-
Displacement parametersBiso mean: 57.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 0 27 1575
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.21
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.6
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.408 110 7.6 %
Rwork0.383 1201 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.HIS
Software
*PLUS
Name: X-PLOR / Version: 3.8 / 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_deg18.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18
LS refinement shell
*PLUS
Rfactor obs: 0.383

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