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- PDB-2x9d: Tet repressor (class D) in complex with iso-7-chlortetracycline -

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Basic information

Entry
Database: PDB / ID: 2x9d
TitleTet repressor (class D) in complex with iso-7-chlortetracycline
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / GENE REGULATION / HTH-MOTIF / DNA-BINDING PROTEIN / 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 / 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
ISO-7-CHLORTETRACYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsVolkers, G. / Hinrichs, W.
Citation
Journal: J.Med.Chem. / Year: 2011
Title: Recognition of Drug Degradation Products by Target Proteins: Isotetracycline Binding to Tet Repressor.
Authors: Volkers, G. / Petruschka, L. / Hinrichs, W.
#1: Journal: Science / Year: 1994
Title: Structure of the Tet Repressor-Tetracycline Complex and Regulation of Antibiotic Resistance.
Authors: Hinrichs, W. / Kisker, C. / Duvel, M. / Muller, A. / Tovar, K. / Hillen, W. / Saenger, W.
History
DepositionMar 15, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionMar 23, 2011ID: 1DU7
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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

Downloads & links

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Assembly

Deposited unit
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9096
Polymers23,2881
Non-polymers6215
Water1,15364
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,81812
Polymers46,5772
Non-polymers1,24110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6070 Å2
ΔGint-102.2 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.253, 68.253, 179.271
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 / TET REPRESSOR


Mass: 23288.334 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-208 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C-TERMINUS REMOVED FOR BETTER CRYSTALLIZATION / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWH1590 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RB791 / References: UniProt: P0ACT4
#2: Chemical ChemComp-ITC / ISO-7-CHLORTETRACYCLINE / (4S,4AS,6S,8AS)-6-[(1S)-7-CHLORO-4-HYDROXY-1-METHYL-3-OXO-1,3-DIHYDRO-2-BENZOFURAN-1-YL]-4-(DIMETHYLAMINO)-3,8A-DIHYDROXY-1,8-DIOXO-1,4,4A,5,6,7,8,8A-OCTAHYDRONAPHTHALENE-2-CARBOXAMIDE


Mass: 478.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23ClN2O8
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 2 TO SER
Sequence detailsA2S CLONING ARTEFACT

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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: 2.27 Å3/Da / Density % sol: 45.3 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 0.002ML PROTEIN/COMPLEX (0.050 ML TETR(D) (C = 17.3 MG/ML)50 ML 2MM ISO-CLTC) PLUS ML BUFFER (50 MM TRIS PH 8, 1.1 M (NH4)2SO4, 100 MM NACL, 10 MM MGCL2) HANGING DROP AGAINST 0.5 ML BUFFER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.979
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Mar 26, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.34→63.7 Å / Num. obs: 9121 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.48 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.7
Reflection shellResolution: 2.34→2.39 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.78 / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TCT

2tct


Resolution: 2.34→63.76 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.904 / SU B: 28.675 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R: 0.576 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 153-164 ARE DISORDERED. THE TRACING OF THE TURN RESIDUES. LEU 101 TO PRO 105 IS AMBIGUOUS BECAUSE OF WEAK ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27974 912 10 %RANDOM
Rwork0.23366 ---
obs0.23826 8209 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--1.52 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 2.34→63.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 37 64 1645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211608
X-RAY DIFFRACTIONr_bond_other_d0.0010.021079
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9992185
X-RAY DIFFRACTIONr_angle_other_deg0.94432607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18223.37777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23315275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9131515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02331
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_it0.6181.5968
X-RAY DIFFRACTIONr_mcbond_other0.1191.5395
X-RAY DIFFRACTIONr_mcangle_it1.11921545
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5913640
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4094.5640
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: 2.342→2.403 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 66 -
Rwork0.209 561 -
obs--93.44 %
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)
14.6168-0.03984.83650.2518-0.24637.11470.0640.28210.02510.05830.1021-0.10690.35060.4065-0.16610.08480.0545-0.04970.1145-0.08890.132518.799428.263313.2592
22.60530.96630.81121.26570.15082.96030.1280.07910.07090.1542-0.080.20080.0228-0.1873-0.0480.1090.07030.01730.1052-0.01390.127824.783532.760439.7894
310.67380.0888-4.9912.88242.76625.0903-0.47231.4617-0.3707-0.0986-0.04410.2270.2035-0.70010.51640.93830.21-0.1210.6022-0.020.868948.586619.635436.1224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 45
2X-RAY DIFFRACTION1A46 - 64
3X-RAY DIFFRACTION2A65 - 93
4X-RAY DIFFRACTION2A101 - 106
5X-RAY DIFFRACTION2A107 - 123
6X-RAY DIFFRACTION2A94 - 100
7X-RAY DIFFRACTION2A124 - 152
8X-RAY DIFFRACTION2A182 - 208
9X-RAY DIFFRACTION3A166 - 181

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