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- PDB-4b1r: Tetracycline repressor class D mutant H100A in complex with iso-7... -

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Basic information

Entry
Database: PDB / ID: 4b1r
TitleTetracycline repressor class D mutant H100A in complex with iso-7- Chlortetracycline
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / ISO-TETRACYCLINE
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
ISO-7-CHLORTETRACYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEltschkner, S. / Palm, G.J. / Schneider, J. / Hinrichs, W.
CitationJournal: To be Published
Title: Tetracycline Repressor Class D Mutant H100A in Complex with Iso-7-Chlortetracycline
Authors: Eltschkner, S. / Palm, G.J. / Schneider, J. / Hinrichs, W.
History
DepositionJul 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 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 / 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 / _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

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Assembly

Deposited unit
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8777
Polymers23,2211
Non-polymers6566
Water1,71195
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,75514
Polymers46,4432
Non-polymers1,31212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6170 Å2
ΔGint-101.6 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.360, 68.360, 179.610
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: 23221.264 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-208 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWH1590 H100A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): RB791 / References: UniProt: P0ACT4
#2: Chemical ChemComp-ITC / ISO-7-CHLORTETRACYCLINE / (4S,4AS,6S,8AS)-6-[(1S)-7-CHLORO-4-HYDROXY-1-METHYL-3-OXO-1,3-DIHYDRO-2-BENZOFURAN-1-YL]-4-(DIMETHYLAMINO)-3,8A-DIHYDROXY-1,8-DIOXO-1,4,4A,5,6,7,8,8A-OCTAHYDRONAPHTHALENE-2-CARBOXAMIDE


Mass: 478.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23ClN2O8
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 100 TO ALA
Sequence detailsN-TERMINAL MET REMOVED RESIDUES 209-218 REMOVED BY CLONING

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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: 2.25 Å3/Da / Density % sol: 45.4 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES, PH 6.5, 0.6 M LI2SO4, 16.7 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8031
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8031 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 16090 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 8 % / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

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

2tct


Resolution: 1.95→19.66 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.324 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25976 760 5 %RANDOM
Rwork0.20571 ---
obs0.20833 14311 93.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.375 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2--1.2 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 38 95 1701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191689
X-RAY DIFFRACTIONr_bond_other_d0.0010.021641
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.9982306
X-RAY DIFFRACTIONr_angle_other_deg0.8533748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1735211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5923.41582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6615296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8681517
X-RAY DIFFRACTIONr_chiral_restr0.0960.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021936
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 68 -
Rwork0.314 1090 -
obs--98.89 %
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)
13.4092-1.73184.01871.4713-0.95947.01440.01520.14890.07720.14470.0535-0.16930.42760.1145-0.06880.1441-0.0752-0.01940.3495-0.0570.268219.054128.5313.9955
21.92791.35770.95721.08070.59433.25220.10990.15150.1490.23460.0720.19060.0775-0.1894-0.18190.32950.13130.04030.24660.02340.319824.931532.831640.4358
332.22045.50873.34712.0785-2.07076.863-0.41921.0030.2175-0.36220.07870.01120.59940.14030.34050.28430.1427-0.06470.1763-0.13390.323749.463720.483336.4473
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 DIFFRACTION2A101 - 106
5X-RAY DIFFRACTION2A107 - 123
6X-RAY DIFFRACTION2A94 - 100
7X-RAY DIFFRACTION2A124 - 152
8X-RAY DIFFRACTION2A182 - 208
9X-RAY DIFFRACTION3A166 - 181

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