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- PDB-1ptf: THE 1.6 ANGSTROMS STRUCTURE OF HISTIDINE-CONTAINING PHOSPHOTRANSF... -

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Basic information

Entry
Database: PDB / ID: 1ptf
TitleTHE 1.6 ANGSTROMS STRUCTURE OF HISTIDINE-CONTAINING PHOSPHOTRANSFER PROTEIN HPR FROM STREPTOCOCCUS FAECALIS
ComponentsHISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / cytoplasm
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 speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsJia, Z. / Quail, W. / Delbaere, L.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: The 1.6 A structure of histidine-containing phosphotransfer protein HPr from Streptococcus faecalis.
Authors: Jia, Z. / Vandonselaar, M. / Hengstenberg, W. / Quail, J.W. / Delbaere, L.T.
#1: Journal: Nature / Year: 1993
Title: Active-Centre Torsion-Angle Strain Revealed in the 1.6 Angstroms Resolution Structure of the Histidine-Containing Phosphocarrier Protein Hpr
Authors: Jia, Z. / Vandonselaar, M. / Quail, J.W. / Delbaere, L.T.J.
History
DepositionOct 4, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 14, 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

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Assembly

Deposited unit
A: HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR


Theoretical massNumber of molelcules
Total (without water)9,3311
Polymers9,3311
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.560, 45.460, 29.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR


Mass: 9330.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / References: UniProt: P07515
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.95 Å3/Da / Density % sol: 36.89 %
Crystal grow
*PLUS
Temperature: 11 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.7 mg/mlprotein1drop
245 %sat1drop(NH4)2SO4
350 %sat1reservoir(NH4)2SO4
4citrate-phosphate buffer1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 9587 / % possible obs: 95 % / Num. measured all: 88281 / Rmerge(I) obs: 0.061

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.6→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.156 -
obs0.156 9481
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms637 0 0 99 736
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.9
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_it2.2472
X-RAY DIFFRACTIONx_mcangle_it3.1043
X-RAY DIFFRACTIONx_scbond_it7.9025
X-RAY DIFFRACTIONx_scangle_it11.8837
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 8 Å / Num. reflection all: 9481 / σ(F): 0 / Rfactor all: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d1.9
X-RAY DIFFRACTIONx_planar_d0.020.047
X-RAY DIFFRACTIONx_plane_restr0.020.014
X-RAY DIFFRACTIONx_chiral_restr0.150.24

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