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- PDB-3pnm: Crystal Structure of E.coli Dha kinase DhaK (H56A) -

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Basic information

Entry
Database: PDB / ID: 3pnm
TitleCrystal Structure of E.coli Dha kinase DhaK (H56A)
ComponentsPTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
KeywordsTRANSFERASE / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


monosaccharide catabolic process / glycerol to glycerone phosphate metabolic process / phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / ketone catabolic process / glycerone kinase activity / carbohydrate phosphorylation / transferase complex / glycerol catabolic process / pyruvate metabolic process ...monosaccharide catabolic process / glycerol to glycerone phosphate metabolic process / phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / ketone catabolic process / glycerone kinase activity / carbohydrate phosphorylation / transferase complex / glycerol catabolic process / pyruvate metabolic process / DNA damage response / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Dihydroxyacetone kinase DhaK, subunit 1 / Dihydroxyacetone kinase; domain 2 / DhaK domain / Dak1 domain / DhaK domain profile. / Dihydroxyacetone kinase; domain 1 / Hypothetical Protein Tm841; Chain: A;domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsShi, R. / McDonald, L. / Matte, A. / Cygler, M. / Ekiel, I. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase.
Authors: Shi, R. / McDonald, L. / Cui, Q. / Matte, A. / Cygler, M. / Ekiel, I.
History
DepositionNov 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
B: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
C: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
D: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK


Theoretical massNumber of molelcules
Total (without water)152,7884
Polymers152,7884
Non-polymers00
Water5,801322
1
A: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
B: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK


Theoretical massNumber of molelcules
Total (without water)76,3942
Polymers76,3942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-13 kcal/mol
Surface area24280 Å2
MethodPISA
2
C: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
D: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK


Theoretical massNumber of molelcules
Total (without water)76,3942
Polymers76,3942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.756, 82.531, 93.068
Angle α, β, γ (deg.)77.930, 77.900, 71.020
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D)

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Components

#1: Protein
PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK


Mass: 38196.922 Da / Num. of mol.: 4 / Mutation: H56N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1200, dhaK, JW5187, ycgT / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P76015, Transferases; Transferring phosphorus-containing groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.75 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG 8000, 0.1M sodium citrate pH 5.6, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorDetector: CCD / Date: Jun 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→41.71 Å / Num. obs: 52242 / % possible obs: 98.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.15 / Χ2: 1.893 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.55-2.6430.50852381.84198
2.64-2.7530.40851951.56998.2
2.75-2.8730.33751831.27498.3
2.87-3.0230.24552181.24898.5
3.02-3.2130.18752081.35598.5
3.21-3.4630.16152191.78598.8
3.46-3.812.90.12552282.20398.8
3.81-4.362.90.152402.69298.9
4.36-5.492.90.07552642.51999.2
5.49-502.90.06252492.52599.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→41.71 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.2094 / WRfactor Rwork: 0.1592 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.854 / SU B: 8.558 / SU ML: 0.187 / SU R Cruickshank DPI: 0.5491 / SU Rfree: 0.2766 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 2657 5.1 %RANDOM
Rwork0.1724 ---
obs0.1753 52147 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.32 Å2 / Biso mean: 20.6131 Å2 / Biso min: 4.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å2-0.37 Å22.06 Å2
2---0.72 Å2-0.63 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.55→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10236 0 0 322 10558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210463
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.96314230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2451361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17425.043462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.085151689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3151552
X-RAY DIFFRACTIONr_chiral_restr0.0920.21635
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217972
X-RAY DIFFRACTIONr_mcbond_it0.7581.56710
X-RAY DIFFRACTIONr_mcangle_it1.498210745
X-RAY DIFFRACTIONr_scbond_it2.1533753
X-RAY DIFFRACTIONr_scangle_it3.7934.53480
LS refinement shellResolution: 2.548→2.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 159 -
Rwork0.232 3494 -
all-3653 -
obs--93 %

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