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- PDB-2fj1: Crystal Structure Analysis of Tet Repressor (class D) in Complex ... -

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Basic information

Entry
Database: PDB / ID: 2fj1
TitleCrystal Structure Analysis of Tet Repressor (class D) in Complex with 7-Chlortetracycline-Nickel(II)
ComponentsTetracycline repressor protein class D
KeywordsTRANSCRIPTION REGULATOR / TRANSCRIPTION REGULATION / helix-turn-helix / metal coordination
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 / 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
7-CHLOROTETRACYCLINE / NICKEL (II) ION / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOrth, P. / Saenger, W. / Palm, G.J. / Hinrichs, W.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2008
Title: Specific binding of divalent metal ions to tetracycline and to the Tet repressor/tetracycline complex.
Authors: Palm, G.J. / Lederer, T. / Orth, P. / Saenger, W. / Takahashi, M. / Hillen, 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. / Duevel, M. / Mueller, A. / Tovar, K. / Hillen, W. / Saenger, W.
History
DepositionDec 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9326
Polymers23,2881
Non-polymers6445
Water1,838102
1
A: Tetracycline repressor protein class D
hetero molecules

A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,86512
Polymers46,5772
Non-polymers1,28810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area8520 Å2
ΔGint-96 kcal/mol
Surface area19390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.937, 68.937, 180.893
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: 23288.334 Da / Num. of mol.: 1 / Fragment: residues 2-208 / Mutation: A2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Plasmid: PWH610 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 DELTA H1 DELTA TRP / References: UniProt: P0ACT4
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CTC / 7-CHLOROTETRACYCLINE


Mass: 478.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23ClN2O8 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.58 M Ammonium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 5, 1997
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→64.5 Å / Num. all: 10706 / Num. obs: 10706 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 32.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.258 Å / Mean I/σ(I) obs: 3.2 / Num. unique all: 751 / Rsym value: 0.268

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TCT

2tct


Resolution: 2.2→64.55 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.467 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.24 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 544 4.8 %RANDOM
Rwork0.14638 ---
all0.14942 10706 --
obs0.14942 10706 97.62 %-
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: 33.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 37 102 1780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0211750
X-RAY DIFFRACTIONr_bond_other_d0.0020.021595
X-RAY DIFFRACTIONr_angle_refined_deg2.4641.9852387
X-RAY DIFFRACTIONr_angle_other_deg1.14633688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395214
X-RAY DIFFRACTIONr_chiral_restr0.1670.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021979
X-RAY DIFFRACTIONr_gen_planes_other0.010.02363
X-RAY DIFFRACTIONr_nbd_refined0.2420.2412
X-RAY DIFFRACTIONr_nbd_other0.2520.21720
X-RAY DIFFRACTIONr_nbtor_other0.1130.21034
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.213
X-RAY DIFFRACTIONr_mcbond_it1.6091.51054
X-RAY DIFFRACTIONr_mcangle_it3.04221690
X-RAY DIFFRACTIONr_scbond_it4.0943696
X-RAY DIFFRACTIONr_scangle_it6.7454.5697
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 38
Rwork0.208 713

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