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- PDB-2vpr: Tet repressor class H in complex with 5a,6- anhydrotetracycline-Mg -

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Basic information

Entry
Database: PDB / ID: 2vpr
TitleTet repressor class H in complex with 5a,6- anhydrotetracycline-Mg
ComponentsTETRACYCLINE RESISTANCE REPRESSOR PROTEIN
KeywordsTRANSCRIPTION / METAL-BINDING / ANTIBIOTIC RESISTANCE / TRANSCRIPTION REGULATOR / TRANSCRIPTION REGULATION DNA-BINDING
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
5A,6-ANHYDROTETRACYCLINE / Tetracycline repressor protein class H / TetR(H)
Similarity search - Component
Biological speciesPASTEURELLA MULTOCIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSchuldt, L. / Palm, G. / Hinrichs, W.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Tet Repressor Induction by Tetracycline: A Molecular Dynamics, Continuum Electrostatics, and Crystallographic Study
Authors: Aleksandrov, A. / Schuldt, L. / Hinrichs, W. / Simonson, T.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural Basis of Gene Regulation by the Tetracycline Inducible Tet Repressor-Operator System
Authors: Orth, P. / Schnappinger, D. / Hillen, W. / Saenger, W. / Hinrichs, W.
#2: Journal: Science / Year: 1994
Title: Structure of the Tet Repressor - Tetracycline Complex and Regulation of Antibiotic Resistance
Authors: Hinrichs, W. / Kisker, C. / Duevel, M. / Mueller, A. / Tovar, K. / Hillen, W. / Saenger, W.
History
DepositionMar 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TETRACYCLINE RESISTANCE REPRESSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7584
Polymers23,2111
Non-polymers5473
Water32418
1
A: TETRACYCLINE RESISTANCE REPRESSOR PROTEIN
hetero molecules

A: TETRACYCLINE RESISTANCE REPRESSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5168
Polymers46,4232
Non-polymers1,0946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5700 Å2
ΔGint-68 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.361, 108.744, 68.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein TETRACYCLINE RESISTANCE REPRESSOR PROTEIN / TETRACYCLINE REPRESSOR CLASS H


Mass: 23211.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PASTEURELLA MULTOCIDA (bacteria) / Plasmid: PWH1590 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RB791 / References: UniProt: Q799E2, UniProt: P51561*PLUS
#2: Chemical ChemComp-TDC / 5A,6-ANHYDROTETRACYCLINE


Mass: 426.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N2O7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 7.5
Details: 3.31 MG/ML TETR(H), 100 UL 2 MM ANTC,100 UL TETR(H),0.5 UL 3 M MGCL2, 20 % PEG1500, 0.1 M NAHEPES PH 7.5, 2 UL RESERVOIR LSG PLUS 2 UL PROTEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8084
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2005 / Details: MIRRORS
RadiationMonochromator: SI (111), HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8084 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 7669 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 69

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TCT

2tct


Resolution: 2.49→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.9 / SU B: 21.494 / SU ML: 0.239 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.938 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 741 9.7 %RANDOM
Rwork0.201 ---
obs0.209 6898 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å20 Å20 Å2
2---2.81 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.49→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 37 18 1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221613
X-RAY DIFFRACTIONr_bond_other_d0.0010.021053
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9872193
X-RAY DIFFRACTIONr_angle_other_deg1.00332587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.71125.34273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.09315280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.048156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02300
X-RAY DIFFRACTIONr_nbd_refined0.2470.2451
X-RAY DIFFRACTIONr_nbd_other0.1870.21064
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2804
X-RAY DIFFRACTIONr_nbtor_other0.0950.2789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3650.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.691.51064
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04421571
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5093720
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.334.5622
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: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 58
Rwork0.221 497
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)
14.36120.4487-0.923112.99810.43493.7324-0.04660.0344-0.0753-0.0849-0.02151.23430.2594-0.42480.0681-0.0579-0.0754-0.05150.01910.05180.0927-18.696139.286825.9809
21.63850.3767-0.13821.55671.04411.411-0.0222-0.0264-0.12270.09510.1435-0.09620.15550.1491-0.12130.02190.0324-0.02440.02790.0004-0.02637.25545.802829.784
35.53341.0590.41817.022-0.54241.8549-0.47070.66970.35540.3650.74741.1323-0.55870.5378-0.27670.1828-0.05290.1032-0.04030.0172-0.0436.593971.78425.4414
41.2719-0.33240.12982.2803-0.83240.3039-0.0568-0.5302-1.2001-0.3602-0.17320.4638-1.08860.02940.23-0.04010.03-0.13150.2939-0.01410.21056.081341.306933.5896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 46
2X-RAY DIFFRACTION2A47 - 157
3X-RAY DIFFRACTION2A182 - 205
4X-RAY DIFFRACTION3A165 - 181
5X-RAY DIFFRACTION4A1206

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