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- PDB-3pnk: Crystal Structure of E.coli Dha kinase DhaK -

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Basic information

Entry
Database: PDB / ID: 3pnk
TitleCrystal Structure of E.coli Dha kinase DhaK
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
PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7124
Polymers76,5282
Non-polymers1842
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-22 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.833, 91.507, 73.232
Angle α, β, γ (deg.)90.000, 89.960, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

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


Mass: 38263.992 Da / Num. of mol.: 2
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.62 %
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: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorDetector: CCD / Date: Dec 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.21→49.83 Å / Num. obs: 30618 / % possible obs: 93.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.122 / Χ2: 0.993 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.21-2.292.70.45726340.945181.1
2.29-2.383.20.40128830.919188.4
2.38-2.494.10.42630260.999192
2.49-2.6250.38230190.999192.4
2.62-2.785.80.31229921.001192.2
2.78-360.22130170.999192.5
3-3.35.90.14931301195.2
3.3-3.7860.11232620.998199.4
3.78-4.766.40.08532980.998199.9
4.76-506.40.07333571199.7

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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
Starting model: pdb entry 1OI2

1oi2


Resolution: 2.21→49.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1982 / WRfactor Rwork: 0.1937 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8636 / SU B: 11.435 / SU ML: 0.14 / SU R Cruickshank DPI: 0.3879 / SU Rfree: 0.1939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1561 5.1 %RANDOM
Rwork0.1719 ---
obs0.1738 30579 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.98 Å2 / Biso mean: 30.6636 Å2 / Biso min: 15.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.01 Å2
2---0.56 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.21→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 12 165 5485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225423
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9667374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5925.043230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70915872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7421526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024104
X-RAY DIFFRACTIONr_nbd_refined0.2040.22423
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.21
X-RAY DIFFRACTIONr_mcbond_it0.6351.53579
X-RAY DIFFRACTIONr_mcangle_it1.08125598
X-RAY DIFFRACTIONr_scbond_it1.7832066
X-RAY DIFFRACTIONr_scangle_it2.8394.51775
LS refinement shellResolution: 2.212→2.269 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 92 -
Rwork0.219 1742 -
all-1834 -
obs--76.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1258-0.10240.16110.8764-0.13620.82090.0142-0.01740.05930.007-0.017-0.0317-0.02930.02630.0028-0.075-0.0005-0.0121-0.0613-0.0089-0.02914.3756-0.343824.8006
20.09360.0077-0.16770.7723-0.1570.80950.01210.0268-0.0649-0.0146-0.0073-0.02950.01810.0278-0.0048-0.0692-0.0081-0.0155-0.058-0.014-0.028414.3207-30.433611.7791
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 366
2X-RAY DIFFRACTION2B12 - 366

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