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- PDB-2xgd: Crystal structure of a designed homodimeric variant T-A(L)A(L) of... -

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Basic information

Entry
Database: PDB / ID: 2xgd
TitleCrystal structure of a designed homodimeric variant T-A(L)A(L) of the tetracycline repressor
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / CHIMERA / TRANSCRIPTION REGULATION / ANTIBIOTIC RESISTANCE
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 B from transposon Tn10 / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5222
Polymers23,4871
Non-polymers351
Water99155
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)47,0444
Polymers46,9732
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area4540 Å2
ΔGint-49.4 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.656, 69.656, 184.328
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 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 136 TO TRP ENGINEERED RESIDUE IN CHAIN A, PHE 197 TO ILE
Sequence detailsENGINEERED VARIANT, NAMELY CHIMERA OF P04483 AND P0ACT4 ( UNIPROT ACCESSION NUMBERS) AND 2 ...ENGINEERED VARIANT, NAMELY CHIMERA OF P04483 AND P0ACT4 ( UNIPROT ACCESSION NUMBERS) AND 2 MUTATIONS. AUTHOR HAS MENTIONED THAT THE C-TERMINUS OF P0ACT4 HAS BEEN TRUNCATED ARTIFICIALLY SINCE THE LATTER HAS 218 RESIDUES IN TOTAL

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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: 48.32 % / Description: 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: 2.25→40 Å / Num. obs: 11142 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.2
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.2 / % possible all: 96.2

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Processing

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

1a6i


Resolution: 2.25→34.84 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 17.216 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.237 / 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
RfactorNum. reflection% reflectionSelection details
Rfree0.25886 890 8 %RANDOM
Rwork0.21686 ---
obs0.22032 10254 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: 48.629 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2--1.93 Å20 Å2
3----3.86 Å2
Refinement stepCycle: LAST / Resolution: 2.25→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 1 55 1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211577
X-RAY DIFFRACTIONr_bond_other_d0.0020.021078
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9652131
X-RAY DIFFRACTIONr_angle_other_deg0.96432617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63823.63677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.37615284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1381514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021741
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
X-RAY DIFFRACTIONr_nbd_refined0.2250.2406
X-RAY DIFFRACTIONr_nbd_other0.190.21019
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2771
X-RAY DIFFRACTIONr_nbtor_other0.0960.2815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1940.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7841.51258
X-RAY DIFFRACTIONr_mcbond_other0.1391.5394
X-RAY DIFFRACTIONr_mcangle_it0.9521536
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4333700
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9944.5595
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: 2.252→2.374 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.308 125 -
Rwork0.256 1414 -
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)
17.6225-4.0028.34173.1777-2.322513.05940.17720.59330.06940.0483-0.1047-0.02950.84310.6291-0.0726-0.1111-0.0052-0.0773-0.0619-0.0973-0.045119.468627.858610.8419
22.10860.30251.91980.04360.216316.3952-0.08910.1724-0.3308-0.2470.01370.45570.6726-1.08090.0754-0.05840.1001-0.0762-0.1651-0.0596-0.048121.810627.872734.6887
37.1590.2291-4.08983.56423.340111.4319-0.00760.68620.2698-0.7174-0.04160.6129-0.7438-0.89780.0492-0.07170.1889-0.0749-0.22170.0107-0.082923.909836.948937.4409
49.33552.8826-0.24814.6179-2.08175.24570.1819-0.3109-0.95550.3062-0.489-0.49770.95871.00210.3072-0.20030.2435-0.1201-0.10870.1623-0.121539.002928.14946.3259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 48
2X-RAY DIFFRACTION2A49 - 95
3X-RAY DIFFRACTION3A96 - 152
4X-RAY DIFFRACTION4A166 - 208

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