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- PDB-2qmh: structure of V267F mutant HprK/P -

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Basic information

Entry
Database: PDB / ID: 2qmh
Titlestructure of V267F mutant HprK/P
ComponentsHPr kinase/phosphorylase
KeywordsTRANSFERASE / V267F mutation / ATP-binding / Carbohydrate metabolism / Kinase / Magnesium / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Serine/threonine-protein kinase / METAL BINDING PROTEIN
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
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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HPr kinase/phosphorylase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChaptal, V. / Vincent, F. / Gueguen-Chaignon, V. / Poncet, S. / Deutscher, J. / Nessler, S. / Morera, S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural Analysis of the Bacterial HPr Kinase/Phosphorylase V267F Mutant Gives Insights into the Allosteric Regulation Mechanism of This Bifunctional Enzyme.
Authors: Chaptal, V. / Vincent, F. / Gueguen-Chaignon, V. / Monedero, V. / Poncet, S. / Deutscher, J. / Nessler, S. / Morera, S.
History
DepositionJul 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HPr kinase/phosphorylase
B: HPr kinase/phosphorylase
C: HPr kinase/phosphorylase
D: HPr kinase/phosphorylase
E: HPr kinase/phosphorylase
F: HPr kinase/phosphorylase
G: HPr kinase/phosphorylase
H: HPr kinase/phosphorylase
I: HPr kinase/phosphorylase
J: HPr kinase/phosphorylase
K: HPr kinase/phosphorylase
L: HPr kinase/phosphorylase


Theoretical massNumber of molelcules
Total (without water)272,73212
Polymers272,73212
Non-polymers00
Water63135
1
A: HPr kinase/phosphorylase
B: HPr kinase/phosphorylase
C: HPr kinase/phosphorylase
D: HPr kinase/phosphorylase
E: HPr kinase/phosphorylase
F: HPr kinase/phosphorylase


Theoretical massNumber of molelcules
Total (without water)136,3666
Polymers136,3666
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17750 Å2
MethodPISA
2
G: HPr kinase/phosphorylase
H: HPr kinase/phosphorylase
I: HPr kinase/phosphorylase
J: HPr kinase/phosphorylase
K: HPr kinase/phosphorylase
L: HPr kinase/phosphorylase


Theoretical massNumber of molelcules
Total (without water)136,3666
Polymers136,3666
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.059, 106.368, 106.486
Angle α, β, γ (deg.)119.50, 90.02, 89.96
Int Tables number1
Space group name H-MP1
Detailsthe biological unit is a hexamer

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Components

#1: Protein
HPr kinase/phosphorylase / HPrK/P / HPrSer / kinase/phosphorylase / HPr kinase/phosphatase


Mass: 22727.695 Da / Num. of mol.: 12 / Fragment: C-terminal domain (128-319) / Mutation: V267F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: hprK / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q9RE09, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases, Transferases; Transferring phosphorus-containing groups; Phosphotransferases ...References: UniProt: Q9RE09, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: MPD, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2006 / Details: 0.97
RadiationMonochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 81301 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 13
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JB1
Resolution: 2.6→19.43 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.88 / SU B: 12.29 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.618 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29773 4029 5 %RANDOM
Rwork0.22078 ---
obs0.22467 76341 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.564 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.02 Å2-0.01 Å2
2---0.02 Å2-0.09 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15556 0 0 35 15591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02215783
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.96521370
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.10751990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14924.412714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.333152792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.66315111
X-RAY DIFFRACTIONr_chiral_restr0.1370.22545
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211697
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2730.27289
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.210666
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2564
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.296
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2131.510174
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.145216045
X-RAY DIFFRACTIONr_scbond_it2.40736115
X-RAY DIFFRACTIONr_scangle_it3.8944.55325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 266 -
Rwork0.313 5402 -
obs--97.14 %

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