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- PDB-2hxr: Structure of the ligand binding domain of E. coli CynR, a transcr... -

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Basic information

Entry
Database: PDB / ID: 2hxr
TitleStructure of the ligand binding domain of E. coli CynR, a transcriptional regulator controlling cyanate metabolism
ComponentsHTH-type transcriptional regulator cynR
KeywordsTRANSCRIPTION / CynR transcriptional regulator LysR crystal structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
HTH-type transcriptional regulator CynR, PBP2 domain / D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...HTH-type transcriptional regulator CynR, PBP2 domain / D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator CynR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsSinger, A.U. / Cuff, M.E. / Evdokimova, E. / Kagan, O. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of CynR, a transcriptional regulator, both in the presence and absence of sodium azide, its activator ligand
Authors: Singer, A.U. / Evdokimova, E. / Cuff, M.E. / Kagan, O. / Edwards, A.M. / Joachimiak, A. / Savchenko, A.
History
DepositionAug 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator cynR
B: HTH-type transcriptional regulator cynR


Theoretical massNumber of molelcules
Total (without water)52,8122
Polymers52,8122
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-15 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.913, 98.555, 62.236
Angle α, β, γ (deg.)90.00, 104.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HTH-type transcriptional regulator cynR / Cyn operon transcriptional activator


Mass: 26405.803 Da / Num. of mol.: 2 / Fragment: residues 63-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cynR / Plasmid: p15Tv-lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27111
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.24 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium formate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97885, 0.97874
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 22, 2005
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978851
20.978741
ReflectionResolution: 2.05→20 Å / Num. all: 57793 / Num. obs: 57793 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 3.1 Å2 / Rsym value: 0.066 / Net I/σ(I): 13.8
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 4233 / Rsym value: 0.269 / % possible all: 65.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2196467.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2780 4.9 %RANDOM
Rwork0.239 ---
all0.241 57143 --
obs0.239 56855 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.6945 Å2 / ksol: 0.334972 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-13.53 Å20 Å22.02 Å2
2---2.82 Å20 Å2
3----10.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.05→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 0 348 3471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 380 5.2 %
Rwork0.301 6929 -
obs--69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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