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- PDB-4d7m: TetR(D) in complex with anhydrotetracycline and magnesium -

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Basic information

Entry
Database: PDB / ID: 4d7m
TitleTetR(D) in complex with anhydrotetracycline and magnesium
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / ANTIBIOTIC RESISTANCE / TETR
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 / 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
5A,6-ANHYDROTETRACYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWerten, S. / Dalm, D. / Palm, G.J. / Hinrichs, W.
CitationJournal: Biochemistry / Year: 2014
Title: Tetracycline Repressor Allostery Does not Depend on Divalent Metal Recognition.
Authors: Werten, S. / Dalm, D. / Palm, G.J. / Grimm, C.C. / Hinrichs, W.
History
DepositionNov 25, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionDec 10, 2014ID: 2XPS
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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)25,0228
Polymers24,3341
Non-polymers6897
Water3,225179
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,04416
Polymers48,6672
Non-polymers1,37714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6900 Å2
ΔGint-112.8 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.628, 65.628, 178.598
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-2057-

HOH

21A-2156-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TETRACYCLINE REPRESSOR PROTEIN CLASS D


Mass: 24333.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWH208 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: P0ACT4

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Non-polymers , 5 types, 186 molecules

#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: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.07 Å3/Da / Density % sol: 40.6 % / Description: NONE
Crystal growpH: 9
Details: 50 MM TRIS-HCL PH 9.0, 1 M (NH4)2SO4, 70 MM NACL, 10 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: May 1, 2004 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.55→28.9 Å / Num. obs: 28546 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.5
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 2.94 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRT

2trt


Resolution: 1.55→61.6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.394 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21669 1347 4.7 %RANDOM
Rwork0.17627 ---
obs0.17816 27199 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.096 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.55→61.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 41 179 1861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191781
X-RAY DIFFRACTIONr_bond_other_d0.0010.021692
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9962434
X-RAY DIFFRACTIONr_angle_other_deg0.90733873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.395220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58923.48389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34215303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6381518
X-RAY DIFFRACTIONr_chiral_restr0.2580.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022070
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02426
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_it1.9551.803862
X-RAY DIFFRACTIONr_mcbond_other1.9541.802861
X-RAY DIFFRACTIONr_mcangle_it2.8642.6911088
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7652.071919
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: 1.552→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 98 -
Rwork0.275 1959 -
obs--98.75 %
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)
11.56530.05342.32520.15170.2063.56280.09540.20780.04010.0756-0.1344-0.02150.19470.1860.0390.0987-0.017-0.02450.19420.00470.027318.702927.595113.1312
20.9537-0.02510.30580.20620.25252.00510.01070.0568-0.0684-0.0088-0.00910.04640.2733-0.1546-0.00160.1181-0.0424-0.01250.0518-0.00450.01621.959126.909834.8375
31.3688-0.5727-0.31090.4861-0.0380.80150.00360.0956-0.0539-0.0241-0.00950.0421-0.0128-0.07210.0060.095-0.00350.00910.0557-0.01620.009824.866232.374735.0569
41.34850.3191-0.49940.2227-0.17411.1442-0.0111-0.0735-0.11250.0167-0.0325-0.00260.1690.11940.04360.14640.0028-0.00060.05520.00010.014538.837126.801442.8274
51.52462.3132-3.579811.3243-5.49448.41640.03190.0684-0.01830.1625-0.08280.0739-0.0889-0.13540.05090.0557-0.0183-0.02970.06350.01060.019719.494734.25134.8083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 106
3X-RAY DIFFRACTION3A107 - 160
4X-RAY DIFFRACTION4A161 - 208
5X-RAY DIFFRACTION5A222 - 223

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