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- PDB-1fu0: CRYSTAL STRUCTURE ANALYSIS OF THE PHOSPHO-SERINE 46 HPR FROM ENTE... -

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Basic information

Entry
Database: PDB / ID: 1fu0
TitleCRYSTAL STRUCTURE ANALYSIS OF THE PHOSPHO-SERINE 46 HPR FROM ENTEROCOCCUS FAECALIS
ComponentsPHOSPHOCARRIER PROTEIN HPR
KeywordsSIGNALING PROTEIN / Phospho-Serine HPr / PTS System
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 / SYNCHROTRON / Resolution: 1.9 Å
AuthorsAudette, G.F. / Engelmann, R. / Hengstenberg, W. / Deutscher, J. / Hayakawa, K. / Quail, J.W. / Delbaere, L.T.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The 1.9 A resolution structure of phospho-serine 46 HPr from Enterococcus faecalis.
Authors: Audette, G.F. / Engelmann, R. / Hengstenberg, W. / Deutscher, J. / Hayakawa, K. / Quail, J.W. / Delbaere, L.T.
History
DepositionSep 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOCARRIER PROTEIN HPR
B: PHOSPHOCARRIER PROTEIN HPR


Theoretical massNumber of molelcules
Total (without water)18,5632
Polymers18,5632
Non-polymers00
Water1,63991
1
A: PHOSPHOCARRIER PROTEIN HPR


Theoretical massNumber of molelcules
Total (without water)9,2811
Polymers9,2811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOCARRIER PROTEIN HPR


Theoretical massNumber of molelcules
Total (without water)9,2811
Polymers9,2811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.520, 43.200, 60.750
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99872, 0.02055, 0.04623), (0.01595, 0.99509, -0.09769), (-0.04801, -0.09682, -0.99414)
Vector: 11.087, -23.54104, 32.35572)
DetailsThe biological assembly is a monomer

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Components

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


Mass: 9281.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / Strain: 26487 / References: UniProt: P07515
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 31.74 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 2.8M sodium-potassium phosphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 287.0K
Crystal
*PLUS
Density % sol: 31.3 %
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
21.4 Msodium potassium phosphate1drop
32.8 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 10043 / Num. obs: 10043 / % possible obs: 95.1 % / Redundancy: 4.23 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Num. unique all: 447 / % possible all: 84.3
Reflection
*PLUS
Num. measured all: 42471
Reflection shell
*PLUS
% possible obs: 84.3 % / Num. unique obs: 447 / Num. measured obs: 1668

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Simulated Annealing
RfactorNum. reflection% reflectionSelection details
Rfree0.239 496 5 %RANDOM
Rwork0.178 ---
all0.178 10043 --
obs0.178 10043 100 %-
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 0 91 1383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.59
X-RAY DIFFRACTIONx_dihedral_angle_d22.93
X-RAY DIFFRACTIONx_improper_angle_d1.15
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.93
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.15

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