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- PDB-3pnq: Crystal Structure of E.coli Dha kinase DhaK (H56N) complex with Dha -

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Basic information

Entry
Database: PDB / ID: 3pnq
TitleCrystal Structure of E.coli Dha kinase DhaK (H56N) complex with Dha
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 / transferase complex / carbohydrate phosphorylation / 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 / transferase complex / carbohydrate phosphorylation / 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 ...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
Dihydroxyacetone / PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,0505
Polymers152,9604
Non-polymers901
Water8,665481
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)76,4802
Polymers76,4802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-13 kcal/mol
Surface area23840 Å2
MethodPISA
2
C: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
D: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5703
Polymers76,4802
Non-polymers901
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-9 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.232, 101.073, 99.349
Angle α, β, γ (deg.)90.000, 89.950, 90.000
Int Tables number4
Space group name H-MP1211
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: 38239.949 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: Sugar ChemComp-2HA / Dihydroxyacetone


Type: saccharide / Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.61
11h,-k,-l20.39
ReflectionResolution: 2.2→49.67 Å / Num. obs: 81917 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Χ2: 1.132 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.283.60.20580770.93498.4
2.28-2.373.60.17580741.02698.4
2.37-2.483.60.16681161.0398.8
2.48-2.613.60.14881381.05599.3
2.61-2.773.70.13181791.17799.5
2.77-2.993.70.11381881.26299.7
2.99-3.293.80.09182581.20599.9
3.29-3.7640.07682231.088100
3.76-4.7440.06282741.3299.8
4.74-5040.05483901.16999.7

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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: 2.2→49.67 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2107 / WRfactor Rwork: 0.1954 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7567 / SU B: 4.953 / SU ML: 0.125 / SU R Cruickshank DPI: 0.0519 / SU Rfree: 0.0385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 4149 5.1 %RANDOM
Rwork0.1995 ---
obs0.2005 81897 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.51 Å2 / Biso mean: 20.7449 Å2 / Biso min: 4.32 Å2
Baniso -1Baniso -2Baniso -3
1--12.77 Å20 Å23.71 Å2
2--31.8 Å20 Å2
3----19.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10100 0 6 481 10587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210305
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.96514009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31251337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76425.153458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.817151672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9181552
X-RAY DIFFRACTIONr_chiral_restr0.0940.21607
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217853
X-RAY DIFFRACTIONr_mcbond_it0.7191.56604
X-RAY DIFFRACTIONr_mcangle_it1.313210573
X-RAY DIFFRACTIONr_scbond_it2.04533701
X-RAY DIFFRACTIONr_scangle_it3.344.53433
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 283 -
Rwork0.21 5402 -
all-5685 -
obs--93.38 %

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