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- PDB-1cm2: STRUCTURE OF HIS15ASP HPR AFTER HYDROLYSIS OF RINGED SPECIES. -

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Basic information

Entry
Database: PDB / ID: 1cm2
TitleSTRUCTURE OF HIS15ASP HPR AFTER HYDROLYSIS OF RINGED SPECIES.
ComponentsHISTIDINE-CONTAINING PROTEIN
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / SUCCINIMIDE / ISOIMIDE
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / antisigma factor binding / regulation of carbon utilization / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme regulator activity / enzyme activator activity / cytosol
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / PTS HPR domain serine phosphorylation site signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNapper, S. / Delbaere, L.T.J. / Waygood, E.B.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The aspartyl replacement of the active site histidine in histidine-containing protein, HPr, of the Escherichia coli Phosphoenolpyruvate:Sugar phosphotransferase system can accept and donate a ...Title: The aspartyl replacement of the active site histidine in histidine-containing protein, HPr, of the Escherichia coli Phosphoenolpyruvate:Sugar phosphotransferase system can accept and donate a phosphoryl group. Spontaneous dephosphorylation of acyl-phosphate autocatalyzes an internal cyclization
Authors: Napper, S. / Delbaere, L.T. / Waygood, E.B.
History
DepositionMay 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTIDINE-CONTAINING PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,1061
Polymers9,1061
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.920, 45.970, 27.220
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HISTIDINE-CONTAINING PROTEIN / PHOSPHOCARRIER PROTEIN HPR


Mass: 9106.273 Da / Num. of mol.: 1 / Mutation: HIS15ASP
Source method: isolated from a genetically manipulated source
Details: THE STRUCTURE IS THAT OF HIS15ASP HPR WHICH HAS UNDERGONE HYDROLYSIS FROM A HIGH-PI RINGED SPECIES OF THE PROTEIN WHICH IS BELIEVED TO INVOLVE SUCCINIMIDE OR ISOIMIDE FORMATION.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PTSH / Plasmid: PUC19 / Cell line (production host): ESK108 / Gene (production host): PTSH / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA04
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.73 Å3/Da / Density % sol: 28.75 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 14 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mcitrate phosphate1reservoir
220-25 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 1
DetectorType: WEISSENBERG
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 6570 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Rsym value: 9.7

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE E. COLI HPR

Resolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.2 --
obs0.2 6570 97.5 %
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms783 0 0 143 926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.2 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 / Num. reflection obs: 5670
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.4

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