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- PDB-3frq: Structure of the macrolide biosensor protein, MphR(A), with eryth... -

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Basic information

Entry
Database: PDB / ID: 3frq
TitleStructure of the macrolide biosensor protein, MphR(A), with erythromcyin
ComponentsRepressor protein MphR(A)
KeywordsDNA BINDING PROTEIN / macrolide antibiotic. repressor / biosensor / erythromycin / Strptomyces / natural products / biosynthesis / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


transferase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ERYTHROMYCIN A / Erythromycin resistance repressor protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsZheng, J. / Sagar, V. / Smolinsky, A. / Bourke, C. / LaRonde-LeBlanc, N. / Cropp, T.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and function of the macrolide biosensor protein, MphR(A), with and without erythromycin
Authors: Zheng, J. / Sagar, V. / Smolinsky, A. / Bourke, C. / LaRonde-LeBlanc, N. / Cropp, T.A.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Repressor protein MphR(A)
B: Repressor protein MphR(A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,51212
Polymers43,4202
Non-polymers2,09110
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-71 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.294, 61.201, 134.642
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 Repressor protein MphR(A)


Mass: 21710.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mphR(A) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EVJ6
#2: Chemical ChemComp-ERY / ERYTHROMYCIN A


Mass: 733.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H67NO13 / Comment: antibiotic*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.141.47
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop5.535-40% (W/V) PEG 3350, 0.2M MgCl2, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop5.535-40% (W/V) PEG 3350, 0.2M MgCl2, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2008
RadiationMonochromator: Konzu HLD8-24 filter monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.76→67.27 Å / Num. all: 35359 / Num. obs: 35192 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→67.27 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.35 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 1844 5 %RANDOM
Rwork0.18102 ---
obs0.18303 35192 99.53 %-
all-35359 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.002 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.76→67.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 140 235 3243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223139
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5542.0174290
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9395389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.39522.932133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16215520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0491531
X-RAY DIFFRACTIONr_chiral_restr0.1050.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022287
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21625
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22244
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2190
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0851.51939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56523038
X-RAY DIFFRACTIONr_scbond_it2.55631335
X-RAY DIFFRACTIONr_scangle_it3.8754.51242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.759→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 127 -
Rwork0.232 2518 -
obs--98.47 %
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)
10.9751-0.30070.30880.87020.05460.6601-0.0109-0.05690.04610.0090.016-0.07050.01740.1095-0.0051-0.05080.00810.0037-0.0106-0.0088-0.051611.7666.756522.4942
20.9013-0.03280.18231.46920.71721.1357-0.11760.05070.0097-0.2060.03650.2549-0.077-0.1180.0811-0.0235-0.0232-0.042-0.0350.0104-0.0234-8.92437.37028.6324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 189
2X-RAY DIFFRACTION2B6 - 189

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