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- PDB-4aux: Tet repressor class D in complex with 9-nitrotetracycline -

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Basic information

Entry
Database: PDB / ID: 4aux
TitleTet repressor class D in complex with 9-nitrotetracycline
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / ANTIBIOTIC
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
Chem-XTC / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOrth, P. / Saenger, W. / Hinrichs, W.
Citation
Journal: To be Published
Title: Tet Repressor Class D in Complex with 9-Nitrotetracycline and Magnesium
Authors: Orth, P. / Saenger, W. / 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
DepositionMay 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1May 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 1.2May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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 / pdbx_struct_conn_angle / struct_conn / 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 / _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)23,8275
Polymers23,2721
Non-polymers5554
Water99155
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,65410
Polymers46,5452
Non-polymers1,1098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6560 Å2
ΔGint-88 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.100, 69.100, 182.930
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


Mass: 23272.334 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Variant: DELTA H1 DELTA TRP / Plasmid: PWH904 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): DELTA H1 DELTA TRP / References: UniProt: P0ACT4
#2: Chemical ChemComp-XTC / (4S,4aS,5aR,12aS)-4-(dimethylamino)-3,10,12,12a-tetrahydroxy-9-nitro-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide / 9-NITROTETRACYCLINE


Mass: 459.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O9
#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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M (NH4)2S04, 200 MM NACL, 5 MM MGCL2 AND 20 MM TRIS-HCL, PH 8.0 WITH 10 MG/ML TETR, 2 MM 9-NITROTC AND 5 MM MGCL2, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.2→17.8 Å / Num. obs: 11066 / % possible obs: 98.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 37
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.2 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0027refinement
DENZOdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TCT

2tct


Resolution: 2.25→17.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 20.809 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A LOOP CONNECTING RESIDUES 155-165 IS HIGHLY DISORDERED SHOWING FRAGMENTED ELECTRON DENSITY AND HIGH B-FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25834 832 7.7 %RANDOM
Rwork0.20877 ---
obs0.21275 9996 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.25→17.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 36 55 1731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191705
X-RAY DIFFRACTIONr_bond_other_d0.0010.021633
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9942320
X-RAY DIFFRACTIONr_angle_other_deg0.79333733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4875206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24623.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93115289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0221516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.25→2.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 68 -
Rwork0.353 698 -
obs--96.6 %
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)
15.7566-1.38568.22631.4954-1.564912.09180.13840.29640.04450.0831-0.1066-0.1920.39210.2051-0.03180.1672-0.1051-0.02840.37-0.07320.268819.217628.88314.1705
21.8134-0.1892-1.03151.35121.049110.08360.0630.2248-0.06280.18730.05340.24910.2382-0.4222-0.11640.18590.0716-0.04120.2026-0.02520.27320.488931.941937.299
332.97256.15111.85949.31570.3910.2406-0.39951.697-0.6832-0.62620.2742-0.05680.15350.08990.12530.52520.10890.04490.4199-0.00980.390751.210420.702935.9079
45.01960.2895-0.10683.08561.41085.72410.28610.3031-0.01970.3661-0.14720.00250.0877-0.064-0.13890.26510.0837-0.01930.07810.02630.175730.995634.332643.7956
50.0110.2757-0.08357.6144-2.17340.6496-0.0376-0.0109-0.0066-0.4281-0.081-0.54370.25640.00970.11870.67720.0342-0.02630.6887-0.03190.680249.076823.154521.6771
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 DIFFRACTION2A94 - 100
5X-RAY DIFFRACTION2A101 - 106
6X-RAY DIFFRACTION2A107 - 123
7X-RAY DIFFRACTION2A222 - 223
8X-RAY DIFFRACTION3A163 - 181
9X-RAY DIFFRACTION4A124 - 155
10X-RAY DIFFRACTION4A182 - 208
11X-RAY DIFFRACTION5A156 - 162

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