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- PDB-1ko7: X-ray structure of the HPr kinase/phosphatase from Staphylococcus... -

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Basic information

Entry
Database: PDB / ID: 1ko7
TitleX-ray structure of the HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution
ComponentsHpr kinase/phosphatase
KeywordsTRANSFERASE / HYDROLASE / Protein kinase / phosphotransfer / protein phosphatase / dual activity / product / substrate
Function / homology
Function and homology information


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 / phosphorelay sensor kinase activity / protein serine/threonine/tyrosine kinase activity / carbohydrate metabolic process / protein serine/threonine kinase activity / magnesium ion binding / ATP binding
Similarity search - Function
HprK N-terminal domain-like / HPr(Ser) kinase/phosphorylase, N-terminal / HPr Serine kinase N terminus / HPr(Ser) kinase/phosphorylase / HPr kinase/phosphorylase, C-terminal / HPr Serine kinase C-terminal domain / HPr(Ser) kinase/phosphorylase-like, N-terminal domain superfamily / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...HprK N-terminal domain-like / HPr(Ser) kinase/phosphorylase, N-terminal / HPr Serine kinase N terminus / HPr(Ser) kinase/phosphorylase / HPr kinase/phosphorylase, C-terminal / HPr Serine kinase C-terminal domain / HPr(Ser) kinase/phosphorylase-like, N-terminal domain superfamily / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / HPr kinase/phosphorylase
Similarity search - Component
Biological speciesStaphylococcus xylosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMarquez, J.A. / Hasenbein, S. / Koch, B. / Fieulaine, S. / Nessler, S. / Hengstenberg, W. / Scheffzek, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution: Mimicking the product/substrate of the phospho transfer reactions.
Authors: Marquez, J.A. / Hasenbein, S. / Koch, B. / Fieulaine, S. / Nessler, S. / Russell, R.B. / Hengstenberg, W. / Scheffzek, K.
History
DepositionDec 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Remark 600HETEROGEN Two phosphate ions in the P-loop regions mimic the substrate/product state of the phospho ...HETEROGEN Two phosphate ions in the P-loop regions mimic the substrate/product state of the phospho transfer reactions

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hpr kinase/phosphatase
B: Hpr kinase/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3178
Polymers70,7472
Non-polymers5706
Water5,260292
1
B: Hpr kinase/phosphatase
hetero molecules

B: Hpr kinase/phosphatase
hetero molecules

B: Hpr kinase/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,97612
Polymers106,1213
Non-polymers8559
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area8740 Å2
ΔGint-101 kcal/mol
Surface area39900 Å2
MethodPISA
2
A: Hpr kinase/phosphatase
hetero molecules

A: Hpr kinase/phosphatase
hetero molecules

A: Hpr kinase/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,97612
Polymers106,1213
Non-polymers8559
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area8510 Å2
ΔGint-102 kcal/mol
Surface area39210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.240, 152.240, 194.686
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-471-

HOH

DetailsThe biologycally relevant structure is an hexamer formed by three equivalent dimers that lay in adjacent asymmetric units. Symmop 2, Shift -1-1 0 Symmop 3, Shift 0-1 0

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Components

#1: Protein Hpr kinase/phosphatase


Mass: 35373.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus xylosus (bacteria) / Gene: HPRK / Plasmid: pET11a (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) (Stratagene)
References: UniProt: Q9S1H5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M SODIUM-POTASSIUM PHOSPHATE PH 7.6, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
21.6 Msodium potassium phosphate1reservoirpH7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.99867
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2001 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99867 Å / Relative weight: 1
ReflectionResolution: 1.95→64.9 Å / Num. obs: 62908 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 6 % / Rsym value: 0.084 / Net I/σ(I): 13.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.338 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 381615 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 99.8 % / Num. unique obs: 4551 / Num. measured obs: 25052 / Rmerge(I) obs: 0.374

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Processing

Software
NameClassification
CNSrefinement
ProDCdata collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1jb1

1jb1


Resolution: 1.95→64.9 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 6286 10 %random
Rwork0.226 ---
all-62857 --
obs-62857 98.9 %-
Solvent computationBsol: 46.7021 Å2 / ksol: 0.380427 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→64.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4504 0 30 292 4826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 1038 10 %
Rwork0.237 9345 -
obs-9345 99.9 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.226 / Lowest resolution: 50 Å / Num. reflection obs: 62899
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_bond_d0.0056
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / % reflection Rfree: 10 % / Rfactor Rwork: 0.237 / Rfactor obs: 0.237

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