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- PDB-3hfu: Crystal structure of the ligand binding domain of E. coli CynR wi... -

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Basic information

Entry
Database: PDB / ID: 3hfu
TitleCrystal structure of the ligand binding domain of E. coli CynR with its specific effector azide
ComponentsHTH-type transcriptional regulator cynR
KeywordsTRANSCRIPTION / CynR / LysR transcriptional activiator / effector / azide / Activator / Cytoplasm / DNA-binding / Repressor / Transcription regulation
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
AZIDE ION / HTH-type transcriptional regulator CynR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSinger, A.U. / Evdokimova, E. / Kagan, O. / Dong, A. / Edwards, A.M. / Savchenko, A.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the ligand binding domain of E. coli CynR with its specific effector azide
Authors: Singer, A.U. / Evdokimova, E. / Kagan, O. / Cuff, M.E. / Edwards, A.M. / Joachimiak, A. / Savchenko, A.
History
DepositionMay 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
C: HTH-type transcriptional regulator cynR
D: HTH-type transcriptional regulator cynR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,91510
Polymers105,6234
Non-polymers2926
Water8,665481
1
A: HTH-type transcriptional regulator cynR
C: HTH-type transcriptional regulator cynR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9585
Polymers52,8122
Non-polymers1463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HTH-type transcriptional regulator cynR
D: HTH-type transcriptional regulator cynR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9585
Polymers52,8122
Non-polymers1463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.176, 98.363, 86.272
Angle α, β, γ (deg.)90, 103.769, 90
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26405.803 Da / Num. of mol.: 4 / Fragment: UNP residues 63-299
Source method: isolated from a genetically manipulated source
Details: TEV cleavage following purification / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0338, cynR, JW5894 / Plasmid: p15Tvlic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-Plus RP / References: UniProt: P27111
#2: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG5000 monomethyl ether (MME) plus 100 mM Tris 8.5, cryoprotected in 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 8, 2006 / Details: mirrors
RadiationMonochromator: VARIMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 44622 / Num. obs: 44532 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 55.588 Å2 / Rsym value: 0.111 / Net I/σ(I): 17.78
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 3.09 / Num. unique all: 4444 / % possible all: 99.75

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HXR

2hxr


Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 1527 -Random
Rwork0.2229 ---
all0.2255 31043 --
obs-30756 99.1 %-
Displacement parametersBiso mean: 41.526 Å2
Baniso -1Baniso -2Baniso -3
1-12.454 Å20 Å2-1.67 Å2
2--6.366 Å20 Å2
3----18.82 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6281 0 20 481 6782
LS refinement shellResolution: 2.6→2.63 Å
RfactorNum. reflection
Rfree0.3555 47
Rwork0.3059 -
obs-980

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