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- PDB-1opd: HISTIDINE-CONTAINING PROTEIN (HPR), MUTANT WITH SER 46 REPLACED B... -

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Basic information

Entry
Database: PDB / ID: 1opd
TitleHISTIDINE-CONTAINING PROTEIN (HPR), MUTANT WITH SER 46 REPLACED BY ASP (S46D)
ComponentsHISTIDINE-CONTAINING PROTEIN
KeywordsPHOSPHOTRANSFERASE / HISTIDINE
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 / Resolution: 1.5 Å
AuthorsNapper, S. / Delbaere, L. / Waygood, B.
Citation
Journal: Biochemistry / Year: 1996
Title: Mutation of serine-46 to aspartate in the histidine-containing protein of Escherichia coli mimics the inactivation by phosphorylation of serine-46 in HPrs from gram-positive bacteria.
Authors: Napper, S. / Anderson, J.W. / Georges, F. / Quail, J.W. / Delbaere, L.T. / Waygood, E.B.
#1: Journal: Biochemistry / Year: 1996
Title: Influence of N-CAP Mutations on the Structure and Stability of Escherichia Coli Hpr
Authors: Thapar, R. / Nicholson, E.M. / Rajagopal, P. / Waygood, E.B. / Scholtz, J.M. / Klevit, R.E.
History
DepositionAug 1, 1996Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTIDINE-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2542
Polymers9,1581
Non-polymers961
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.850, 27.330, 27.600
Angle α, β, γ (deg.)66.90, 75.71, 70.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HISTIDINE-CONTAINING PROTEIN / HPR


Mass: 9158.327 Da / Num. of mol.: 1 / Mutation: S46D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ESK108 / Plasmid: PUC19 / Gene (production host): PTSH / Production host: Escherichia coli (E. coli) / Strain (production host): ESK108 / References: UniProt: P0AA04
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.82 Å3/Da / Density % sol: 32.57 %
Crystal grow
*PLUS
Temperature: 14 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mcitrate phosphate1reservoir
246-50 %satammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.927
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 21, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionNum. obs: 10525 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.029
Reflection
*PLUS
Highest resolution: 1.5 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.5→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.234 -
Rwork0.182 -
obs0.182 9806
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms643 0 5 225 873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.001
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_deg2.4
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
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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