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- PDB-4zms: Structure of the full-length response regulator spr1814 in comple... -

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Basic information

Entry
Database: PDB / ID: 4zms
TitleStructure of the full-length response regulator spr1814 in complex with a phosphate analogue and B3C
ComponentsResponse regulator
KeywordsDNA BINDING PROTEIN / Response regulator
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / metal ion binding / cytosol
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / 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-4QT / BERYLLIUM TRIFLUORIDE ION / Response regulator
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChi, Y.M. / Park, A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Structural characterization of the full-length response regulator spr1814 in complex with a phosphate analogue reveals a novel conformational plasticity of the linker region
Authors: Park, A.K. / Lee, J.H. / Chi, Y.M. / Park, H.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator
B: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7667
Polymers46,1912
Non-polymers5745
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-29 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.980, 115.526, 50.073
Angle α, β, γ (deg.)90.000, 92.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Response regulator /


Mass: 23095.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: rr11, spr1814 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DNC2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-4QT / 5-amino-2,4,6-tribromobenzene-1,3-diyl dihydroperoxide


Mass: 393.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4Br3NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate tribasic dihydrate pH 5.0, 30%(v/v) Jeffamine ED-2001 pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9198 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35816 / % possible obs: 96.7 % / Redundancy: 9.1 % / Net I/σ(I): 4.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.817 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 1732 4.84 %
Rwork0.1648 34084 -
obs0.1673 35816 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.13 Å2 / Biso mean: 25.2871 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 1.9→37.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 28 503 3710
Biso mean--38.1 31.59 -
Num. residues----407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183235
X-RAY DIFFRACTIONf_angle_d1.7724370
X-RAY DIFFRACTIONf_chiral_restr0.074521
X-RAY DIFFRACTIONf_plane_restr0.008556
X-RAY DIFFRACTIONf_dihedral_angle_d17.4671238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8954-1.95110.29051140.23522630274489
1.9511-2.01410.28141240.20852785290995
2.0141-2.08610.2631440.19162787293196
2.0861-2.16960.23691360.17752852298897
2.1696-2.26840.21621590.16572847300698
2.2684-2.38790.21061200.16142850297098
2.3879-2.53750.22341600.17062854301498
2.5375-2.73340.22991570.17122855301298
2.7334-3.00830.24871370.17422893303099
3.0083-3.44340.20341510.16122904305599
3.4434-4.33730.1891660.13692878304499
4.3373-37.82420.17571640.14532949311399

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