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- PDB-2xpv: TetR(D) in complex with minocycline and magnesium. -

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Basic information

Entry
Database: PDB / ID: 2xpv
TitleTetR(D) in complex with minocycline and magnesium.
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATOR / HELIX-TURN-HELIX / METAL COORDINATION
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
Chem-MIY / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsDalm, D. / Proft, J. / Palm, G.J. / Hinrichs, W.
Citation
Journal: To be Published
Title: Tetr(D) in Complex with Minocycline.
Authors: Dalm, D. / Palm, G.J. / Proft, J. / 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
DepositionAug 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Atomic model
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)24,05411
Polymers23,2881
Non-polymers76510
Water4,900272
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,10722
Polymers46,5772
Non-polymers1,53120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area9310 Å2
ΔGint-196.3 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.686, 68.686, 178.673
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-2022-

HOH

21A-2025-

HOH

31A-2192-

HOH

41A-2236-

HOH

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Components

#1: Protein TETRACYCLINE REPRESSOR PROTEIN CLASS D / TETRACYCLINE REPRESSOR


Mass: 23288.334 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-208
Source method: isolated from a genetically manipulated source
Details: C-TERMINUS REMOVED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWH 610 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): DELTA H1 DELTA TRP / References: UniProt: P0ACT4
#2: Chemical ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE / Minocycline


Mass: 457.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N3O7 / Comment: medication, antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)- 3,10,12, 12A-TETRAHYDROXY-1,11-DIOXO - ...(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)- 3,10,12, 12A-TETRAHYDROXY-1,11-DIOXO -1,4,4A,5,5A,6,11,12A- OCTAHYDROTETRACENE-2-CARBOXAMIDE (MIY): MINOCYCLINE
Sequence detailsC-TERMINUS (209-218) REMOVED FOR BETTER CRYSTALLIZATION

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 8 / Details: 12% PEG 6000, 2.0 M NACL, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.1
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Apr 6, 2004 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.49→64.55 Å / Num. obs: 32272 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.1
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.1 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TCT

2tct


Resolution: 1.49→64.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.383 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20146 1703 5 %RANDOM
Rwork0.18502 ---
obs0.18585 32272 96.12 %-
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: 17.095 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.49→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 42 272 1893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211746
X-RAY DIFFRACTIONr_bond_other_d0.0010.021174
X-RAY DIFFRACTIONr_angle_refined_deg1.6922.0142387
X-RAY DIFFRACTIONr_angle_other_deg0.93332855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3715219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03523.45284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33115305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3191517
X-RAY DIFFRACTIONr_chiral_restr0.1350.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021987
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02365
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_it1.0341.51053
X-RAY DIFFRACTIONr_mcbond_other0.2971.5426
X-RAY DIFFRACTIONr_mcangle_it1.69721697
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.663693
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9684.5690
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: 1.49→1.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 120 -
Rwork0.258 2328 -
obs--96.72 %

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