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- PDB-4mld: X-ray structure of ComE D58E REC domain from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 4mld
TitleX-ray structure of ComE D58E REC domain from Streptococcus pneumoniae
ComponentsResponse regulator
KeywordsUNKNOWN FUNCTION / protein Dimer / REC / response regulator
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA binding
Similarity search - Function
: / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...: / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsBoudes, M. / Sanchez, D. / Durand, D. / Graille, M. / van Tilbeurgh, H. / Quevillon-Cheruel, S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural insights into the dimerization of the response regulator ComE from Streptococcus pneumoniae.
Authors: Boudes, M. / Sanchez, D. / Graille, M. / van Tilbeurgh, H. / Durand, D. / Quevillon-Cheruel, S.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator
B: Response regulator
C: Response regulator
D: Response regulator


Theoretical massNumber of molelcules
Total (without water)68,9104
Polymers68,9104
Non-polymers00
Water00
1
A: Response regulator
D: Response regulator


Theoretical massNumber of molelcules
Total (without water)34,4552
Polymers34,4552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-9 kcal/mol
Surface area12780 Å2
MethodPISA
2
B: Response regulator
C: Response regulator


Theoretical massNumber of molelcules
Total (without water)34,4552
Polymers34,4552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-10 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.850, 90.850, 140.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Response regulator


Mass: 17227.514 Da / Num. of mol.: 4 / Fragment: REC domain (UNP residues 1-137) / Mutation: D58E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-255 / R6 / Gene: comE, spr2041 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q8DMW5

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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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M potassium thiocynate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2013
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.88→45.4 Å / Num. all: 14844 / Num. obs: 14816 / % possible obs: 99.8 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 19.5 % / Rmerge(I) obs: 0.167 / Rsym value: 0.167 / Net I/σ(I): 21.74

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Processing

Software
NameVersionClassification
APEXdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4B1N

4b1n
PDB Unreleased entry


Resolution: 2.88→45.4 Å / SU ML: 0.43 / σ(F): 1.46 / σ(I): 1.5 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 739 5 %5.0%
Rwork0.195 ---
obs0.1972 14790 99.66 %-
all-14844 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.25 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 58.41 Å2
Baniso -1Baniso -2Baniso -3
1--24.767 Å2-0 Å20 Å2
2---24.767 Å2-0 Å2
3---49.5341 Å2
Refinement stepCycle: LAST / Resolution: 2.88→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4468 0 0 0 4468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034548
X-RAY DIFFRACTIONf_angle_d0.6996122
X-RAY DIFFRACTIONf_dihedral_angle_d13.5131738
X-RAY DIFFRACTIONf_chiral_restr0.051688
X-RAY DIFFRACTIONf_plane_restr0.002774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.10630.35791470.29482786X-RAY DIFFRACTION99
3.1063-3.41880.32431480.23322810X-RAY DIFFRACTION100
3.4188-3.91320.2641470.19392802X-RAY DIFFRACTION100
3.9132-4.92930.20081480.16322813X-RAY DIFFRACTION100
4.9293-45.43060.19511490.18172840X-RAY DIFFRACTION99

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