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- PDB-5lcy: Formaldehyde-Responsive Regulator FrmR E64H variant from Salmonel... -

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Basic information

Entry
Database: PDB / ID: 5lcy
TitleFormaldehyde-Responsive Regulator FrmR E64H variant from Salmonella enterica serovar Typhimurium
ComponentsFrmr
KeywordsTRANSCRIPTION / formaldehyde / zinc / salmonella enterica / frmr / rcnr
Function / homology
Function and homology information


negative 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
Transcriptional repressor FrmR
Similarity search - Component
Biological speciesSalmonella enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.19 Å
AuthorsPohl, E. / Robinson, N. / Osman, D. / Piergentili, C. / Uson, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J017787/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Effectors and Sensory Sites of Formaldehyde-responsive Regulator FrmR and Metal-sensing Variant.
Authors: Osman, D. / Piergentili, C. / Chen, J. / Sayer, L.N. / Uson, I. / Huggins, T.G. / Robinson, N.J. / Pohl, E.
History
DepositionJun 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Frmr
B: Frmr
C: Frmr
D: Frmr


Theoretical massNumber of molelcules
Total (without water)40,8484
Polymers40,8484
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-100 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.790, 25.680, 100.500
Angle α, β, γ (deg.)90.00, 103.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Frmr


Mass: 10211.899 Da / Num. of mol.: 4 / Mutation: E64H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica serovar Typhimurium (bacteria)
Strain: SL1344 / Gene: SL1344_1558 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3NLH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20 mM NaCl, 23 % (w/v) poly(ethylene glycol) 4000, and 10 mM BisTris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.19→29.697 Å / Num. obs: 18039 / % possible obs: 98.5 % / Redundancy: 6.3 % / Net I/σ(I): 12.2 / Num. measured all: 113762
Reflection shellResolution: 2.19→2.25 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.19→29.697 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3115 917 5.1 %
Rwork0.2444 --
obs0.2478 17990 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→29.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 0 103 2790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012811
X-RAY DIFFRACTIONf_angle_d1.1263802
X-RAY DIFFRACTIONf_dihedral_angle_d14.0511110
X-RAY DIFFRACTIONf_chiral_restr0.049438
X-RAY DIFFRACTIONf_plane_restr0.006505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.30540.4491130.38722386X-RAY DIFFRACTION97
2.3054-2.44980.35781340.28452357X-RAY DIFFRACTION97
2.4498-2.63890.31981370.26162418X-RAY DIFFRACTION98
2.6389-2.90420.32181340.26622407X-RAY DIFFRACTION98
2.9042-3.3240.36731280.24742472X-RAY DIFFRACTION99
3.324-4.1860.25911390.20552465X-RAY DIFFRACTION99
4.186-29.70.28561320.22912568X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 67.1678 Å / Origin y: 0.4364 Å / Origin z: 25.5735 Å
111213212223313233
T0.3006 Å20.0269 Å20.0121 Å2-0.2263 Å2-0.0575 Å2--0.2964 Å2
L1.3106 °20.3885 °2-0.4783 °2-1.0037 °2-0.5175 °2--2.6012 °2
S-0.0116 Å °-0.0684 Å °-0.0022 Å °0.0621 Å °0.0815 Å °-0.0703 Å °-0.0037 Å °0.0923 Å °-0.0643 Å °
Refinement TLS groupSelection details: all

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