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- PDB-2xgc: Crystal structure of a designed heterodimeric variant T-A(I)B of ... -

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Basic information

Entry
Database: PDB / ID: 2xgc
TitleCrystal structure of a designed heterodimeric variant T-A(I)B of the tetracycline repressor
Components(TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D) x 2
KeywordsTRANSCRIPTION / CHIMERA / TRANSCRIPTION REGULATION / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / 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 B from transposon Tn10 / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsStiebritz, M.T. / Wengrzik, S. / Richter, J.P. / Muller, Y.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Computational Design of a Chain-Specific Tetracycline Repressor Heterodimer.
Authors: Stiebritz, M.T. / Wengrzik, S. / Klein, D.L. / Richter, J.P. / Srebrzynski, A. / Weiler, S. / Muller, Y.A.
History
DepositionJun 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: 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 B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
B: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D


Theoretical massNumber of molelcules
Total (without water)47,1982
Polymers47,1982
Non-polymers00
Water1,02757
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D

A: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D


Theoretical massNumber of molelcules
Total (without water)46,9732
Polymers46,9732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area4610 Å2
ΔGint-41.9 kcal/mol
Surface area19740 Å2
MethodPISA
2
B: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D

B: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D


Theoretical massNumber of molelcules
Total (without water)47,4222
Polymers47,4222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area4610 Å2
ΔGint-41.9 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.152, 69.152, 183.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2032-

HOH

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Components

#1: Protein TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D


Mass: 23486.723 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-50,51-208 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04483, UniProt: P0ACT4
#2: Protein TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D


Mass: 23710.916 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-50,51-208 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04483, UniProt: P0ACT4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 136 TO TRP ENGINEERED RESIDUE IN CHAIN B, PHE 140 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ALA 136 TO TRP ENGINEERED RESIDUE IN CHAIN B, PHE 140 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 192 TO TRP ENGINEERED RESIDUE IN CHAIN A, LEU 193 TO ILE ENGINEERED RESIDUE IN CHAIN A, PHE 197 TO ILE
Sequence detailsENGINEERED VARIANT, NAMELY CHIMERA OF P04483 AND P0ACT4 ( UNIPROT ACCESSION NUMBERS) AUTHOR HAS ...ENGINEERED VARIANT, NAMELY CHIMERA OF P04483 AND P0ACT4 ( UNIPROT ACCESSION NUMBERS) AUTHOR HAS MENTIONED THAT THE C-TERMINUS OF P0ACT4 HAS BEEN TRUNCATED ARTIFICIALLY SINCE THE LATTER HAS 218 RESIDUES IN TOTAL. FOR B CHAIN THERE IS AN ARTIFICIAL N-TERMINAL EXTENSION PRESENT IN THE PROTEIN.

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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

CrystalDescription: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: RAYONIX / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 12563 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.1
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 12 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A6I

1a6i


Resolution: 2.15→34.59 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.642 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. THE CRYSTAL STRUCTURE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. THE CRYSTAL STRUCTURE CORRESPONDS TO A HETERODIMER WITH CHAINS A AND B. BOTH CHAINS DIFFER AT ONLY 5 POSITIONS. THE DATA HAS BEEN EXPLAINED A BIMODAL DISORDER MODEL IN WHICH BOTH CHAINS ARE PRESENT WITH 0.5 OCCUPANCY IN THE ASYMMETRIC UNIT AT THE SAME TIME.
RfactorNum. reflection% reflectionSelection details
Rfree0.27056 1001 8 %RANDOM
Rwork0.21689 ---
obs0.22121 11559 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: 40.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.84 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 0 57 3143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211623
X-RAY DIFFRACTIONr_bond_other_d0.0020.021104
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9582200
X-RAY DIFFRACTIONr_angle_other_deg1.00132681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5725200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74623.54479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.69315288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3761514
X-RAY DIFFRACTIONr_chiral_restr0.090.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined0.2140.2392
X-RAY DIFFRACTIONr_nbd_other0.1830.21064
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2801
X-RAY DIFFRACTIONr_nbtor_other0.0920.2821
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3470.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8991.51300
X-RAY DIFFRACTIONr_mcbond_other0.1591.5402
X-RAY DIFFRACTIONr_mcangle_it1.08821577
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7223727
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5694.5620
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: 2.15→2.266 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 142 -
Rwork0.252 1639 -
obs--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)
17.494-2.19969.68772.7784-1.262114.05050.14950.4761-0.05120.0106-0.05570.16690.83090.3757-0.0938-0.14730.0226-0.0466-0.0127-0.0606-0.138619.01727.616410.7026
21.6135-0.23193.09820.034-0.350620.5339-0.06220.0383-0.25160.0790.02670.42170.4907-1.44680.0354-0.12550.02460.0093-0.1168-0.0178-0.058621.486528.051234.3918
33.7172-0.2683-2.60662.97661.544212.4396-0.21270.27050.19460.05110.26370.4526-0.6701-1.1004-0.051-0.20160.1197-0.0025-0.15770.0507-0.074523.744437.074837.0572
47.98162.49060.38613.1842-2.52345.25590.0376-0.0293-0.64490.3901-0.3058-0.04821.10750.70650.2682-0.1180.1978-0.0874-0.11410.1387-0.201538.638827.718846.1604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 48
2X-RAY DIFFRACTION2A49 - 95
3X-RAY DIFFRACTION3A96 - 151
4X-RAY DIFFRACTION4A166 - 208

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