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- PDB-1poh: THE 2.0 ANGSTROMS RESOLUTION STRUCTURE OF ESCHERICHIA COLI HISTID... -

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Basic information

Entry
Database: PDB / ID: 1poh
TitleTHE 2.0 ANGSTROMS RESOLUTION STRUCTURE OF ESCHERICHIA COLI HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR: A REDETERMINATION
ComponentsHISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / 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 / 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. ...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. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsJia, Z. / Quail, W. / Delbaere, L.
CitationJournal: J.Biol.Chem. / Year: 1993
Title: The 2.0-A resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination.
Authors: Jia, Z. / Quail, J.W. / Waygood, E.B. / Delbaere, L.T.
History
DepositionOct 19, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3213
Polymers9,1291
Non-polymers1922
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.470, 45.950, 25.860
Angle α, β, γ (deg.)90.00, 104.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR


Mass: 9129.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0AA04
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.73 Å3/Da / Density % sol: 28.97 %
Crystal grow
*PLUS
Temperature: 14 ℃ / pH: 3.7 / Method: unknown
Details: referred to 'El-Kabbani', (1993) J.Biol.Chem., 262, 12926-12929
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
168 %satlithium sulfate11
20.1 Mcitrate11
30.2 M11Na2HPO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. obs: 4023 / % possible obs: 94.1 % / Num. measured all: 20532 / Rmerge(I) obs: 0.03

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.135 -
obs0.135 3958
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms640 0 10 89 739
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.021
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_deg2.9
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_it2.3752
X-RAY DIFFRACTIONx_mcangle_it3.23
X-RAY DIFFRACTIONx_scbond_it8.2375
X-RAY DIFFRACTIONx_scangle_it11.4547
Refinement
*PLUS
Rfactor obs: 0.135
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.054
X-RAY DIFFRACTIONx_planar_d0.050.075
X-RAY DIFFRACTIONx_plane_restr0.020.015
X-RAY DIFFRACTIONx_chiral_restr0.150.18

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