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- PDB-3q7t: 2.15A resolution structure (I41 Form) of the ChxR receiver domain... -

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Basic information

Entry
Database: PDB / ID: 3q7t
Title2.15A resolution structure (I41 Form) of the ChxR receiver domain 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
Atypical response regulator protein ChxR / Transcriptional regulatory protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)28,5674
Polymers28,5212
Non-polymers462
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-28 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.720, 53.720, 190.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-114-

NA

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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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 4 M NaCl, 5 % isopropanol, 0.1 M Na/K Phosphate, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.54 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→29.67 Å / Num. obs: 14560 / % possible obs: 100 % / Redundancy: 3.69 % / Rmerge(I) obs: 0.07 / Χ2: 0.95 / Net I/σ(I): 8.6 / Scaling rejects: 407
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2
2.15-2.233.610.4292.5533814691.16
2.23-2.323.60.3413.3527314541.18
2.32-2.423.650.2773.7522014231.06
2.42-2.553.680.2614.1541614651.01
2.55-2.713.680.2224.8536314470.98
2.71-2.923.720.1735.8548014640.91
2.92-3.213.750.1178.2541914400.83
3.21-3.683.750.0910.9549514550.79
3.68-4.633.760.05718.8557914670.76
4.63-29.653.710.04622.9554914710.84

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.26 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.67 Å
Translation2.5 Å29.67 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.3Ldata scaling
PHASER2.1.4phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→29.67 Å / Occupancy max: 1 / Occupancy min: 0.57 / FOM work R set: 0.8423 / SU ML: 0.25 / σ(F): 1.42 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 733 5.04 %
Rwork0.205 13825 -
obs0.2071 14558 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.465 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 90.6 Å2 / Biso mean: 40.0925 Å2 / Biso min: 18.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.0818 Å2-0 Å2-0 Å2
2---0.0818 Å20 Å2
3---0.1637 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 2 41 1672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081670
X-RAY DIFFRACTIONf_angle_d1.0792266
X-RAY DIFFRACTIONf_chiral_restr0.066261
X-RAY DIFFRACTIONf_plane_restr0.004278
X-RAY DIFFRACTIONf_dihedral_angle_d14.801612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1502-2.31620.28571610.247527552916
2.3162-2.54920.2421410.220627542895
2.5492-2.91780.28151540.21727582912
2.9178-3.6750.23511380.202627652903
3.675-29.67450.2291390.18927932932

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