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- PDB-1oi3: X-ray structure of the dihydroxyacetone kinase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1oi3
TitleX-ray structure of the dihydroxyacetone kinase from Escherichia coli
ComponentsHYPOTHETICAL PROTEIN YCGTHypothesis
KeywordsKINASE / DIHYDROXYACETONE KINASE / YCGT
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 / 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 / OTHER / Resolution: 2 Å
AuthorsSiebold, C. / Garcia-Alles, L.-F. / Erni, B. / Baumann, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: A Mechanism of Covalent Substrate Binding in the X-Ray Structure of Subunit K of the Escherichia Coli Dihydroxyacetone Kinase
Authors: Siebold, C. / Garcia-Alles, L.-F. / Erni, B. / Baumann, U.
History
DepositionJun 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN YCGT
B: HYPOTHETICAL PROTEIN YCGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2574
Polymers79,0652
Non-polymers1922
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.465, 97.364, 86.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPCYSCYSAA20 - 20420 - 204
21ASPASPCYSCYSBB20 - 20420 - 204
12LEULEULYSLYSAA218 - 368216 - 366
22LEULEULYSLYSBB218 - 368216 - 366

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.99962, -0.02733, 0.00426), (-0.02735, 0.99962, -0.00356), (-0.00416, -0.00367, -0.99998)
Vector: 164.82719, 2.59917, 129.23039)

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Components

#1: Protein HYPOTHETICAL PROTEIN YCGT / Hypothesis / DIHYDROXYACETONE KINASE


Mass: 39532.609 Da / Num. of mol.: 2 / Fragment: DIHYDROXYACETONE BINDING SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PMSEH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WA2127 / References: UniProt: P76015, glycerone kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO THE DIHYDROXYACETONE KINASE FAMILY

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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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDetails: OSMIC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 51496 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.7
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.1 / % possible all: 60.6

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2→19.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES 218 TO 222 WERE MODELED AS POLY-ALANINES DUE TO INSUFFICEIENT ELECTRON DENSITY FOR THE SIDE-CHAINS FOR THESE RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1443 2.8 %RANDOM
Rwork0.189 ---
obs0.189 50052 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6 Å20 Å20 Å2
2--1.82 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 10 481 5531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0215106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9586942
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8915668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1610.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.023878
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.22635
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2491
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3190.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9282.53306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9453.55274
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8353.51800
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5894.51668
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11323medium positional0.110.5
21182medium positional0.30.5
11323medium thermal1.542
21182medium thermal1.532
LS refinement shellResolution: 2→2.04 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.221 55
Rwork0.186 1857
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)
10.5520.064-0.268-0.0069-0.00770.69070.0480.07750.05590.0065-0.01450.0008-0.0222-0.1431-0.03350.01390.0183-0.00380.03990.0110.022363.34218.15358.788
20.57840.0211-0.2697-0.00210.05110.36550.0327-0.12190.0582-0.01670.01-0.015-0.02910.1047-0.04270.0175-0.01790.00040.0463-0.02670.0251101.27218.58170.506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 368
2X-RAY DIFFRACTION2B20 - 368

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