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- PDB-1knx: HPr kinase/phosphatase from Mycoplasma pneumoniae -

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Basic information

Entry
Database: PDB / ID: 1knx
TitleHPr kinase/phosphatase from Mycoplasma pneumoniae
ComponentsProbable HPr(Ser) kinase/phosphatase
Keywordstransferase/hydrolase / HPr kinase / Hpr kinase/phosphatase / HPrK/P / kinase / phosphatase / P-loop / WALKER A BOX / CATABOLITE REPRESSION / transferase-hydrolase COMPLEX
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
HPr kinase/phosphorylase
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsAllen, G.S.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of HPr Kinase/Phosphatase from Mycoplasma pneumoniae
Authors: Allen, G.S. / Steinhauer, K. / Hillen, W. / Stulke, J. / Brennan, R.G.
History
DepositionDec 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable HPr(Ser) kinase/phosphatase
B: Probable HPr(Ser) kinase/phosphatase
C: Probable HPr(Ser) kinase/phosphatase
D: Probable HPr(Ser) kinase/phosphatase
E: Probable HPr(Ser) kinase/phosphatase
F: Probable HPr(Ser) kinase/phosphatase


Theoretical massNumber of molelcules
Total (without water)211,6626
Polymers211,6626
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28580 Å2
ΔGint-122 kcal/mol
Surface area73680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.734, 127.845, 170.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Probable HPr(Ser) kinase/phosphatase


Mass: 35276.969 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Production host: Escherichia coli (E. coli)
References: UniProt: P75548, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.9 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 8000, sodium chloride, magnesium chloride, tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5
Details: Steinhauer, K., (2002) Acta Crystallogr., D58, 515.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14 %PEG80001reservoir
220 mM1reservoirMgCl2
350 mMTris-HCl1reservoirpH7.6
40.8 M1reservoirKClor NaCl
57 mg/mlHPrK/P1drop
610 mMTris-HCl1droppH7.5
70.6 M1dropNaCl
81 mMAMPPCP1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.8856
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 91137 / % possible obs: 97.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22
Reflection shellResolution: 2.49→2.59 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.418 / % possible all: 94.8
Reflection
*PLUS
Highest resolution: 2.49 Å / Lowest resolution: 30 Å / Num. measured all: 347151
Reflection shell
*PLUS
% possible obs: 94.8 % / Rmerge(I) obs: 0.418

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Processing

Software
NameVersionClassification
d*TREKdata scaling
d*TREKdata reduction
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→29.22 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 225180.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 4109 5 %RANDOM
Rwork0.227 ---
obs0.224 81806 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.3269 Å2 / ksol: 0.35087 e/Å3
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.71 Å20 Å20 Å2
2---0.41 Å20 Å2
3---8.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14435 0 0 282 14717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.211.5
X-RAY DIFFRACTIONc_mcangle_it4.742
X-RAY DIFFRACTIONc_scbond_it4.972
X-RAY DIFFRACTIONc_scangle_it6.592.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 630 5 %
Rwork0.29 11904 -
obs--85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.49 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS

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