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- PDB-3q7s: 2.1A resolution structure of the ChxR receiver domain containing ... -

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Basic information

Entry
Database: PDB / ID: 3q7s
Title2.1A resolution structure of the ChxR receiver domain containing I3C from Chlamydia trachomatis
ComponentsTranscriptional regulatory protein
KeywordsTRANSCRIPTION / ChxR / receiver domain / transcription factor / OmpR / Chlamydia
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-I3C / Atypical response regulator protein ChxR / Transcriptional regulatory protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å
AuthorsHickey, J. / Lovell, S. / Battaile, K.P. / Hu, L. / Middaugh, C.R. / Hefty, P.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The atypical response regulator protein ChxR has structural characteristics and dimer interface interactions that are unique within the OmpR/PhoB subfamily.
Authors: Hickey, J.M. / Lovell, S. / Battaile, K.P. / Hu, L. / Middaugh, C.R. / Hefty, P.S.
History
DepositionJan 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Jun 6, 2018Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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: Transcriptional regulatory protein
B: Transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1975
Polymers28,5212
Non-polymers1,6773
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-15 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.766, 41.086, 45.069
Angle α, β, γ (deg.)90.000, 106.100, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional regulatory protein


Mass: 14260.336 Da / Num. of mol.: 2 / Fragment: unp residues 2-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: 434/Bu / Gene: CTLon_0888 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0BA84, UniProt: A0A0H3MDW1*PLUS
#2: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 20 % PEG 3350, 0.2 M sodium thiocyanate, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2009 / Details: Osmic Blue double focusing
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Number: 52247 / Rmerge(I) obs: 0.122 / Χ2: 1.78 / D res high: 2.1 Å / D res low: 30 Å / Num. obs: 15613 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.523099.910.0882.6763.3
3.594.5299.610.0922.0993.4
3.143.5999.510.1131.9813.4
2.853.1499.410.1481.9053.4
2.652.8599.210.181.6943.4
2.492.6598.510.2351.6353.4
2.372.4998.210.281.5623.4
2.262.3798.310.3371.4193.4
2.182.2698.510.381.3663.3
2.12.1896.210.4671.3873.2
ReflectionResolution: 2.1→30 Å / Num. all: 15613 / Num. obs: 15613 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1530 / % possible all: 96.2

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
SHELXphasing
SHELXmodel building
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→28.138 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8113 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 785 5.03 %RANDOM
Rwork0.196 ---
obs0.199 15595 98.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.052 Å2 / ksol: 0.436 e/Å3
Displacement parametersBiso max: 84.09 Å2 / Biso mean: 37.2733 Å2 / Biso min: 18.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.4597 Å20 Å2-0.7406 Å2
2--0.4476 Å2-0 Å2
3---0.0121 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 48 77 1812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181781
X-RAY DIFFRACTIONf_angle_d1.6982425
X-RAY DIFFRACTIONf_chiral_restr0.097268
X-RAY DIFFRACTIONf_plane_restr0.009302
X-RAY DIFFRACTIONf_dihedral_angle_d15.89649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.093-2.22410.33641260.26082410253697
2.2241-2.39570.28841150.22552443255898
2.3957-2.63670.27641450.19882427257298
2.6367-3.01780.2451330.18382466259999
3.0178-3.80070.22951300.16425022632100
3.8007-28.14010.24441360.196625622698100

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