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- PDB-4ml3: X-ray structure of ComE D58A REC domain from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 4ml3
TitleX-ray structure of ComE D58A 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: 3.15 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)68,6784
Polymers68,6784
Non-polymers00
Water0
1
A: Response regulator
C: Response regulator


Theoretical massNumber of molelcules
Total (without water)34,3392
Polymers34,3392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-8 kcal/mol
Surface area12900 Å2
MethodPISA
2
B: Response regulator
D: Response regulator


Theoretical massNumber of molelcules
Total (without water)34,3392
Polymers34,3392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.470, 91.470, 134.840
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: 17169.479 Da / Num. of mol.: 4 / Fragment: REC domain (UNP residues 1-137) / Mutation: D58A
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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, 0.2M Sodium formate , pH 7.5, VAPOR DIFFUSION, HANGING 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: Feb 24, 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: 3.15→45.7 Å / Num. all: 11136 / Num. obs: 11099 / % possible obs: 99.67 % / Observed criterion σ(F): 3.16 / Observed criterion σ(I): 3.16 / Redundancy: 9.22 % / Biso Wilson estimate: 65.55 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 15
Reflection shellResolution: 3.15→3.46 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 15 / Num. unique all: 11099 / Rsym value: 0.144 / % possible all: 99.7

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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: 3.15→45.7 Å / SU ML: 0.15 / σ(F): 1.99 / σ(I): 2 / Phase error: 33.2 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflectionSelection details
Rfree0.322 553 4.99 %4.99%
Rwork0.272 ---
obs0.2745 11086 99.58 %-
all-11136 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.909 Å2 / ksol: 0.14 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--24.3346 Å20 Å20 Å2
2---24.3346 Å2-0 Å2
3---48.6691 Å2
Refinement stepCycle: LAST / Resolution: 3.15→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 0 0 4333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044409
X-RAY DIFFRACTIONf_angle_d0.8785926
X-RAY DIFFRACTIONf_dihedral_angle_d14.8021678
X-RAY DIFFRACTIONf_chiral_restr0.061668
X-RAY DIFFRACTIONf_plane_restr0.003741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.46380.3731360.38162596X-RAY DIFFRACTION99
3.4638-3.96480.3511380.28842643X-RAY DIFFRACTION100
3.9648-4.99430.27991380.23622618X-RAY DIFFRACTION100
4.9943-45.73980.3241410.25722676X-RAY DIFFRACTION100

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