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- PDB-4xwj: Histidine-containing phosphocarrier protein (HPr) and antisigma f... -

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Basic information

Entry
Database: PDB / ID: 4xwj
TitleHistidine-containing phosphocarrier protein (HPr) and antisigma factor Rsd complex
Components
  • Phosphocarrier protein HPr
  • Regulator of sigma D
KeywordsTRANSCRIPTION/TRANSFERASE / anti sigma 70 factor / TRANSCRIPTION-TRANSFERASE complex
Function / homology
Function and homology information


positive regulation of nucleotide catabolic process / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / sigma factor antagonist activity / bacterial-type RNA polymerase core enzyme binding / phosphoenolpyruvate-dependent sugar phosphotransferase system / sigma factor antagonist complex / enzyme inhibitor activity ...positive regulation of nucleotide catabolic process / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / sigma factor antagonist activity / bacterial-type RNA polymerase core enzyme binding / phosphoenolpyruvate-dependent sugar phosphotransferase system / sigma factor antagonist complex / enzyme inhibitor activity / stringent response / enzyme regulator activity / enzyme activator activity / negative regulation of DNA-templated transcription / cytoplasm / cytosol
Similarity search - Function
Regulator of RNA polymerase sigma(70) subunit, domain 4 / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ / Regulator of RNA polymerase sigma(70) subunit, Rsd / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ superfamily / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like ...Regulator of RNA polymerase sigma(70) subunit, domain 4 / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ / Regulator of RNA polymerase sigma(70) subunit, Rsd / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ superfamily / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr / Regulator of sigma D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.095 Å
AuthorsUm, S.H. / Seok, Y.J. / Ha, N.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural basis for the sequestration of the anti-sigma (70) factor Rsd from sigma (70) by the histidine-containing phosphocarrier protein HPr.
Authors: Park, Y.H. / Um, S.H. / Song, S. / Seok, Y.J. / Ha, N.C.
History
DepositionJan 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of sigma D
B: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)28,6572
Polymers28,6572
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-6 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.768, 74.768, 72.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Regulator of sigma D


Mass: 19588.105 Da / Num. of mol.: 1 / Fragment: UNP residues 1 -151 / Mutation: A133S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rsd, b3995, JW3959
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0AFX4
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9069.236 Da / Num. of mol.: 1 / Mutation: F2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ptsH, hpr, b2415, JW2408 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AA04, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NaCl, 0.1 M HEPES (pH 7.5), 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13804 / % possible obs: 97.21 % / Redundancy: 15.8 % / Net I/σ(I): 44.43

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
d*TREKdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.095→29.579 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.74 / Phase error: 33.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2989 695 5.04 %
Rwork0.2182 --
obs0.222 13797 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.095→29.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 0 28 1879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191879
X-RAY DIFFRACTIONf_angle_d1.8412539
X-RAY DIFFRACTIONf_dihedral_angle_d17.799692
X-RAY DIFFRACTIONf_chiral_restr0.073296
X-RAY DIFFRACTIONf_plane_restr0.008324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.095-2.25670.3471400.29392574X-RAY DIFFRACTION97
2.2567-2.48370.37051520.29332498X-RAY DIFFRACTION94
2.4837-2.84290.3161410.26782533X-RAY DIFFRACTION95
2.8429-3.58070.30881320.22942696X-RAY DIFFRACTION99
3.5807-29.58190.25491300.1692801X-RAY DIFFRACTION99

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