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- PDB-1qpi: CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qpi
TitleCRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX
Components
  • DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3')
  • DNA (5'-D(*TP*CP*TP*AP*TP*CP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3')
  • PROTEIN (TETRACYCLINE REPRESSOR)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / REPRESSOR-OPERATOR COMPLEX / TRANSCRIPTION-DNA COMPLEX
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
IMIDAZOLE / DNA / DNA (> 10) / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsOrth, P. / Schnappinger, D. / Hillen, W. / Saenger, W. / Hinrichs, W.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system.
Authors: Orth, P. / Schnappinger, D. / Hillen, W. / Saenger, W. / Hinrichs, W.
History
DepositionMay 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3')
N: DNA (5'-D(*TP*CP*TP*AP*TP*CP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3')
A: PROTEIN (TETRACYCLINE REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0774
Polymers32,0083
Non-polymers691
Water73941
1
M: DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3')
N: DNA (5'-D(*TP*CP*TP*AP*TP*CP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3')
A: PROTEIN (TETRACYCLINE REPRESSOR)
hetero molecules

M: DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3')
N: DNA (5'-D(*TP*CP*TP*AP*TP*CP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3')
A: PROTEIN (TETRACYCLINE REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1548
Polymers64,0166
Non-polymers1382
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)38.040, 193.200, 91.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: DNA chain DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3') / TET OPERATOR DNA


Mass: 4577.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA SEQUENCE TAKEN FROM TET OPERATOR CLASS D
#2: DNA chain DNA (5'-D(*TP*CP*TP*AP*TP*CP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3') / TET OPERATOR DNA


Mass: 4599.008 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (TETRACYCLINE REPRESSOR) / REGULATORY PROTEIN TETR


Mass: 22831.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): K12 DELTA H1 DELTA TRP / References: UniProt: P0ACT4
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112.5 %PEG40001reservoiror 12.5 % mPEG5000
2200-300 mMsalt1reservoir
3100-150 mMimidazole1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 28, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→34.5 Å / Num. obs: 12437 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.287 / % possible all: 93.3
Reflection
*PLUS
Lowest resolution: 24.5 Å / Num. obs: 11520 / Num. measured all: 42624 / Biso Wilson estimate: 57.9 Å2
Reflection shell
*PLUS
% possible obs: 94.4 % / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→34.5 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: USED WEIGHTED FULL MATRIX LEAST SQUARE PROCEDURE. THE DNA BASE PAIRS 1, 8 AND 15 ARE NOT PALINDROMIC. IN REFINEMENT THE CENTRAL BASE M 8 WAS MODELED USING ADENINE AND THYMINE WITH 50 % ...Details: USED WEIGHTED FULL MATRIX LEAST SQUARE PROCEDURE. THE DNA BASE PAIRS 1, 8 AND 15 ARE NOT PALINDROMIC. IN REFINEMENT THE CENTRAL BASE M 8 WAS MODELED USING ADENINE AND THYMINE WITH 50 % OCCUPANCY EACH, RESPECTIVELY. BASE M 1 WAS EITHER CYTOSINE OR THYMINE AND BASE M 15 WAS EITHER GUANINE OR ADENINE. DUE TO CLOSE CRYSTAL PACKING CONTACTS THESE TERMINAL BASES WERE FOUND DISORDERED AND WERE MODELED AS CYTOSINE (BASE M 1) AND ADENINE (BASE M 15), RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1166 10 %RANDOM
Rwork0.244 ---
obs0.244 11520 94.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 324 5 41 1921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.6

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