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- PDB-5fo5: Structure of the DNA-binding domain of Escherichia coli methionin... -

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Basic information

Entry
Database: PDB / ID: 5fo5
TitleStructure of the DNA-binding domain of Escherichia coli methionine biosynthesis regulator MetR
ComponentsHTH-TYPE TRANSCRIPTIONAL REGULATOR METR
KeywordsTRANSCRIPTION / HTH / DNA-BINDING / TRANSCRIPTION REGULATION / LYSR-TYPE TRANSCRIPTIONAL REGULATOR / METHIONINE BIOSYNTHESIS / ACTIVATOR / REPRESSOR
Function / homology
Function and homology information


methionine biosynthetic process / amino acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
HTH-type transcriptional regulator MetR, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...HTH-type transcriptional regulator MetR, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator MetR
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPunekar, A.S. / Porter, J. / Urbanowski, M.L. / Stauffer, G.V. / Carr, S.B. / Phillips, S.E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structural Basis for DNA Recognition by the Transcription Regulator Metr.
Authors: Punekar, A.S. / Porter, J. / Carr, S.B. / Phillips, S.E.V.
History
DepositionNov 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Aug 16, 2017Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.3Jan 10, 2024Group: 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_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: HTH-TYPE TRANSCRIPTIONAL REGULATOR METR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4463
Polymers10,3601
Non-polymers862
Water68538
1
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR METR
hetero molecules

A: HTH-TYPE TRANSCRIPTIONAL REGULATOR METR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8936
Polymers20,7202
Non-polymers1734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2260 Å2
ΔGint-40.2 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.760, 55.120, 49.990
Angle α, β, γ (deg.)90.00, 98.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2005-

HOH

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Components

#1: Protein HTH-TYPE TRANSCRIPTIONAL REGULATOR METR


Mass: 10359.946 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, UNP RESIDUES 1-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A9F9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 4

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 34 %
Description: STRUCTURE WAS SOLVED USING MR_ROSETTA IN PHENIX
Crystal growpH: 7.2
Details: 50 MM HEPES PH 7.2, 1.2 M AMMONIUM SULFATE, 200 MM POTASSIUM CHLORIDE, 50 MM MAGNESIUM CHLORIDE

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.16→8.92 Å / Num. obs: 3976 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 15.64 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 21.28
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 11.03 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FXQ

3fxq


Resolution: 2.16→8.921 Å / SU ML: 0.15 / σ(F): 1.48 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 398 10.02 %
Rwork0.1907 --
obs0.195 3973 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→8.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms689 0 5 38 732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002727
X-RAY DIFFRACTIONf_angle_d0.529986
X-RAY DIFFRACTIONf_dihedral_angle_d12.311463
X-RAY DIFFRACTIONf_chiral_restr0.033115
X-RAY DIFFRACTIONf_plane_restr0.003131

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