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- PDB-1kkm: L.casei HprK/P in complex with B.subtilis P-Ser-HPr -

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Basic information

Entry
Database: PDB / ID: 1kkm
TitleL.casei HprK/P in complex with B.subtilis P-Ser-HPr
Components
  • HprK protein
  • PHOSPHOCARRIER PROTEIN HPR
KeywordsTRANSFERASE / HYDROLASE/TRANSPORT PROTEIN / phosphorylation / protein kinase / bacteria / protein/protein interaction / phosphoserine / HYDROLASE-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


regulation of carbohydrate utilization / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / regulation of carbohydrate metabolic process / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate-dependent sugar phosphotransferase system / phosphorelay sensor kinase activity / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
HPr(Ser) kinase/phosphorylase / HPr(Ser) kinase/phosphorylase, N-terminal / HPr Serine kinase N terminus / HPr kinase/phosphorylase, C-terminal / HPr Serine kinase C-terminal domain / HPr(Ser) kinase/phosphorylase-like, N-terminal domain superfamily / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like ...HPr(Ser) kinase/phosphorylase / HPr(Ser) kinase/phosphorylase, N-terminal / HPr Serine kinase N terminus / HPr kinase/phosphorylase, C-terminal / HPr Serine kinase C-terminal domain / HPr(Ser) kinase/phosphorylase-like, N-terminal domain superfamily / 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. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphocarrier protein HPr / HPr kinase/phosphorylase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
Bacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFieulaine, S. / Morera, S. / Poncet, S. / Galinier, A. / Janin, J. / Deutscher, J. / Nessler, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr.
Authors: Fieulaine, S. / Morera, S. / Poncet, S. / Mijakovic, I. / Galinier, A. / Janin, J. / Deutscher, J. / Nessler, S.
History
DepositionDec 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HprK protein
B: HprK protein
C: HprK protein
H: PHOSPHOCARRIER PROTEIN HPR
I: PHOSPHOCARRIER PROTEIN HPR
J: PHOSPHOCARRIER PROTEIN HPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,79612
Polymers100,3916
Non-polymers4056
Water3,081171
1
A: HprK protein
B: HprK protein
C: HprK protein
H: PHOSPHOCARRIER PROTEIN HPR
I: PHOSPHOCARRIER PROTEIN HPR
J: PHOSPHOCARRIER PROTEIN HPR
hetero molecules

A: HprK protein
B: HprK protein
C: HprK protein
H: PHOSPHOCARRIER PROTEIN HPR
I: PHOSPHOCARRIER PROTEIN HPR
J: PHOSPHOCARRIER PROTEIN HPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,59224
Polymers200,78212
Non-polymers81012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_775-y+2,-x+2,-z+1/31
Buried area32360 Å2
ΔGint-335 kcal/mol
Surface area58020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.832, 80.832, 252.488
Angle α, β, γ (deg.)90, 90, 120
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein HprK protein


Mass: 22679.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: PTSK / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): NM522
References: UniProt: Q9RE09, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Protein PHOSPHOCARRIER PROTEIN HPR / HISTIDINE-CONTAINING PROTEIN


Mass: 10783.985 Da / Num. of mol.: 3 / Mutation: G85R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PTSH / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): NM522 / References: UniProt: P08877
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-400, Hepes, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
128 %PEG4001reservoir
2100 mMHEPES-Na1reservoirpH7.5
3200 mM1reservoirCaCl2
40.25 mMHprK/P monomer1drop
50.5 mMHPr1drop
610 mMPPi1droppresence or absence

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2001
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 23597 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 5.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2339 / Rsym value: 0.146 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 274803 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.146

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JB1 and 1SPH

1jb1

1sph


Resolution: 2.8→30 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1133 -random
Rwork0.2 ---
all-23689 --
obs-23472 99.1 %-
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5862 0 18 171 6051
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.37
LS refinement shellResolution: 2.8→2.84 Å / Rfactor Rfree: 0.4 / Rfactor Rwork: 0.352
Refinement
*PLUS
Rfactor Rfree: 0.257 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.4 / Rfactor Rwork: 0.352

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