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- PDB-3b6c: Crystal structure of the Streptomyces coelicolor TetR family prot... -

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Basic information

Entry
Database: PDB / ID: 3b6c
TitleCrystal structure of the Streptomyces coelicolor TetR family protein ActR in complex with (S)-DNPA
ComponentsActII protein
KeywordsTRANSCRIPTION / transcriptional repressor / DNA-binding protein / TetR family / actinorhodin / (S)-DNPA / ligand / Transcription regulation
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 / 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 ...Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / 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
Chem-SDN / ActII protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWillems, A.R. / Junop, M.S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA.
Authors: Willems, A.R. / Tahlan, K. / Taguchi, T. / Zhang, K. / Lee, Z.Z. / Ichinose, K. / Junop, M.S. / Nodwell, J.R.
History
DepositionOct 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _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: ActII protein
B: ActII protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2605
Polymers50,4012
Non-polymers8593
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.969, 79.396, 103.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ActII protein / Putative transcriptional regulatory protein


Mass: 25200.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: M145 / Gene: actII / Plasmid: pPROEX-HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53901
#2: Chemical ChemComp-SDN / [(3S)-9-hydroxy-1-methyl-10-oxo-4,10-dihydro-3H-benzo[g]isochromen-3-yl]acetic acid / 4,10-dihydro-9-hydroxy-1-methyl-10-oxo-3-H-naphtho-[2,3-c]-pyran-3-(S)-acetic acid


Mass: 286.279 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H14O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE CA INDEX NUMBER OF COMPOUND SDN IS 224586-86-1.

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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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% PEG4000, 91mM sodium acetate, 45mM Bis-Tris, 23mM KCl, 9.1mM taurine, 4.6mM Tris, 0.45mM DTT and, after dehydration, less than 100 ug (S)-DNPA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2006 / Details: collimating and focusing mirrors
RadiationMonochromator: Si (111) 2 crystals (not a channel-cut) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.23 Å / Num. obs: 19458 / % possible obs: 92.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.63 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.47 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 4.3 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
d*TREKdata reduction
d*TREKdata scaling
CCP46.0.0phasing
Coot0.1.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2OPT

2opt


Resolution: 2.3→41.85 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.892 / SU B: 22.324 / SU ML: 0.267 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.236 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28703 743 5 %RANDOM
Rwork0.24392 ---
obs0.24605 14054 70.04 %-
all-19458 --
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: 83.439 Å2
Baniso -1Baniso -2Baniso -3
1--5 Å20 Å20 Å2
2--5.96 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 66 146 3294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213199
X-RAY DIFFRACTIONr_bond_other_d0.0020.023
X-RAY DIFFRACTIONr_angle_refined_deg0.922.0154341
X-RAY DIFFRACTIONr_angle_other_deg9.26239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09923.088136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.24515531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6851531
X-RAY DIFFRACTIONr_chiral_restr0.0780.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022413
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.30.31715
X-RAY DIFFRACTIONr_nbd_other0.4190.32
X-RAY DIFFRACTIONr_nbtor_refined0.3350.52254
X-RAY DIFFRACTIONr_nbtor_other0.2450.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.5263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.360
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4310.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.35422003
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.40433188
X-RAY DIFFRACTIONr_scbond_it1.82921196
X-RAY DIFFRACTIONr_scangle_it2.8131153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 26 -
Rwork0.327 685 -
obs--46.11 %
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)
12.60690.3061-3.16711.4435-1.11814.2432-0.122-0.1185-0.1380.0681-0.1184-0.0653-0.16490.12670.2404-0.0193-0.0399-0.07210.03980.0234-0.0239-7.0679-10.2235-7.1095
210.90130.67991.26350.0674-0.1842.9109-0.1450.41590.05920.1021-0.0645-0.01060.12160.03690.2096-0.0128-0.0514-0.013-0.054-0.05880.064-28.6895-11.3779-1.2513
34.6332-1.4839-1.41322.3122-1.54212.597-0.15690.47740.18130.2801-0.00680.12-0.3738-0.06540.1637-0.0316-0.0326-0.0458-0.0552-0.0121-0.0388-31.5264-4.3231-2.4954
410.816-1.65776.09019.66832.58647.221.01-0.6051-0.41330.3493-0.2161-0.19721.04210.1828-0.79380.1432-0.12550.0163-0.1214-0.1026-0.1947-29.825-7.162531.0533
56.8872-5.67221.21995.8658-2.48582.0528-0.3651-0.2185-0.06120.290.15420.19980.4488-0.83570.21090.0767-0.0589-0.0045-0.017-0.0962-0.0365-37.0181-9.42429.2379
65.6592.04694.99623.5211-2.274910.4035-0.47110.97440.633-0.17390.0927-0.0855-0.10511.31720.3784-0.1307-0.17340.09660.21650.1388-0.1181-8.037113.4724.7055
712.47861.70242.08820.6184-0.85784.1940.0551-0.20530.69590.4176-0.26120.3403-0.28830.11790.20610.0143-0.01310.1149-0.1992-0.10690.01-33.0158.810921.8409
83.86641.81090.27172.6418-1.01193.94480.11180.16380.06640.0959-0.24950.23530.11230.39110.13770.0110.01480.0817-0.1248-0.0214-0.0342-29.89234.37516.993
92.6225-0.9367-1.86851.91471.89282.29050.29140.65340.4886-0.11-0.17610.0077-0.7296-0.5489-0.1153-0.05050.0556-0.04540.08150.1164-0.0365-33.53934.9226-5.1477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA28 - 913 - 66
2X-RAY DIFFRACTION2AA92 - 13067 - 105
3X-RAY DIFFRACTION3AA131 - 177106 - 152
4X-RAY DIFFRACTION4AA190 - 218165 - 193
5X-RAY DIFFRACTION5AA219 - 241194 - 216
6X-RAY DIFFRACTION6BB29 - 764 - 51
7X-RAY DIFFRACTION7BB77 - 10752 - 82
8X-RAY DIFFRACTION8BB108 - 17783 - 152
9X-RAY DIFFRACTION9BB189 - 242164 - 217

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