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- PDB-4d7n: TetR(D) in complex with anhydrotetracycline and potassium -

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Basic information

Entry
Database: PDB / ID: 4d7n
TitleTetR(D) in complex with anhydrotetracycline and potassium
ComponentsTETRACYCLINE REPRESSOR, CLASS D
KeywordsTRANSCRIPTION / REPRESSOR / ANTIBIOTIC RESISTANCE / TETR
Function / homologyTetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / : / 5A,6-ANHYDROTETRACYCLINE / :
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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: 2XPT
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Other
Revision 1.3Jul 17, 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 / 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.ptnr1_symmetry / _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, CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9808
Polymers24,3341
Non-polymers6467
Water2,810156
1
A: TETRACYCLINE REPRESSOR, CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR, CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,96016
Polymers48,6672
Non-polymers1,29314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6590 Å2
ΔGint-94.4 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.065, 68.065, 178.909
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-301-

K

21A-2028-

HOH

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Components

#1: Protein TETRACYCLINE REPRESSOR, 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: A0A017KEE3
#2: Chemical ChemComp-TDC / 5A,6-ANHYDROTETRACYCLINE


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.23 Å3/Da / Density % sol: 44.9 % / Description: NONE
Crystal growpH: 8 / Details: 13% PEG 6000, 2 M KCL, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Dec 16, 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: 1.76→27.1 Å / Num. obs: 20998 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.5
Reflection shellResolution: 1.76→1.87 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.28 / % possible all: 91.5

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Processing

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

2trt


Resolution: 1.76→63.62 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.562 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22507 1059 5 %RANDOM
Rwork0.18943 ---
obs0.19123 19932 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2--0.75 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.76→63.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 37 156 1750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191629
X-RAY DIFFRACTIONr_bond_other_d0.0010.021569
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9912213
X-RAY DIFFRACTIONr_angle_other_deg0.88533580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3645195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89423.45781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1815283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9371516
X-RAY DIFFRACTIONr_chiral_restr0.2050.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
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_it1.9442.069784
X-RAY DIFFRACTIONr_mcbond_other1.9422.069783
X-RAY DIFFRACTIONr_mcangle_it2.8263.093979
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8812.442845
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: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.553 64 -
Rwork0.617 1202 -
obs--81.1 %
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)
12.2127-0.42022.19140.38160.35754.17720.06880.13240.07720.04410.0535-0.09560.21320.2813-0.12220.0420.0022-0.02590.1196-0.04420.08118.939428.502213.4081
20.9404-0.1077-0.04250.46980.00493.01930.02160.1737-0.12780.0058-0.04440.0960.24790.00720.02290.08790.026-0.01550.098-0.03470.073422.600128.463135.5122
32.3745-0.8951-0.121.10090.75971.620.05870.16220.0263-0.0793-0.04230.0448-0.1121-0.069-0.01630.09060.06040.00420.0742-0.00810.071822.994936.083437.8531
41.51430.1725-0.14490.66810.11710.59370.04930.0237-0.16470.0915-0.12810.08790.1576-0.02140.07870.17020.0326-0.00680.0851-0.00790.061338.465828.537644.3785
50.1927-0.92890.07918.53140.70091.41990.05050.0392-0.00590.0599-0.1516-0.0687-0.0404-0.06090.10120.06290.0244-0.0210.0381-0.00460.035820.629136.094435.0364
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 106
3X-RAY DIFFRACTION3A107 - 152
4X-RAY DIFFRACTION4A165 - 208
5X-RAY DIFFRACTION5A222 - 223

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