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- PDB-5lbm: The asymmetric tetrameric structure of the formaldehyde sensing t... -

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Basic information

Entry
Database: PDB / ID: 5lbm
TitleThe asymmetric tetrameric structure of the formaldehyde sensing transcriptional repressor FrmR from Escherichia coli
ComponentsTranscriptional repressor FrmR
KeywordsTRANSCRIPTION / CsoR/RcnR Escherichia coli FrmR methylene bridge
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
Metal-sensitive repressor, helix protomer / Metal-sensitive transcriptional repressor / Metal-sensitive repressor, helix protomer superfamily / Metal-sensitive transcriptional repressor / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMYL GROUP / Transcriptional repressor FrmR
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBisson, C. / Baker, P.J. / Green, J. / Chivers, P.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L008114/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J014443/1 United Kingdom
CitationJournal: Sci Rep / Year: 2016
Title: The mechanism of a formaldehyde-sensing transcriptional regulator.
Authors: Denby, K.J. / Iwig, J. / Bisson, C. / Westwood, J. / Rolfe, M.D. / Sedelnikova, S.E. / Higgins, K. / Maroney, M.J. / Baker, P.J. / Chivers, P.T. / Green, J.
History
DepositionJun 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor FrmR
B: Transcriptional repressor FrmR
C: Transcriptional repressor FrmR
D: Transcriptional repressor FrmR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7706
Polymers41,7104
Non-polymers602
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-98 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.069, 82.069, 55.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Transcriptional repressor FrmR


Mass: 10427.528 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: frmR, Z0457, ECs0412 / Plasmid: pET22a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8X5J3
#2: Chemical ChemComp-FOR / FORMYL GROUP / Aldehyde


Mass: 30.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O

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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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M MgCl2, 0.1 M Na cacodylate pH 6.5 and 31 % PEG 2000 Protein buffered in: 50mM Hepes pH 7.5 and 0.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→55.25 Å / Num. obs: 11450 / % possible obs: 100 % / Redundancy: 5.3 % / Rpim(I) all: 0.038 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.2 / Rpim(I) all: 0.499 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
xia2data reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→55.25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 14.808 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.368 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26628 567 5 %RANDOM
Rwork0.20879 ---
obs0.2117 10865 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----1.26 Å2
Refinement stepCycle: 1 / Resolution: 2.7→55.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 2 0 2746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192766
X-RAY DIFFRACTIONr_bond_other_d0.0020.022748
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9793708
X-RAY DIFFRACTIONr_angle_other_deg0.9823.0016270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6885342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68622.778144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80415524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7641544
X-RAY DIFFRACTIONr_chiral_restr0.0850.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023132
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02632
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_it3.5287.6181382
X-RAY DIFFRACTIONr_mcbond_other3.5277.6181381
X-RAY DIFFRACTIONr_mcangle_it5.55411.411718
X-RAY DIFFRACTIONr_mcangle_other5.55311.411719
X-RAY DIFFRACTIONr_scbond_it3.7198.3091384
X-RAY DIFFRACTIONr_scbond_other3.7198.311384
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.16712.2331990
X-RAY DIFFRACTIONr_long_range_B_refined8.49190.5563084
X-RAY DIFFRACTIONr_long_range_B_other8.4990.5693085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 51 -
Rwork0.298 813 -
obs--100 %

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