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- PDB-1oi2: X-ray structure of the dihydroxyacetone kinase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1oi2
TitleX-ray structure of the dihydroxyacetone kinase from Escherichia coli
ComponentsHYPOTHETICAL PROTEIN YCGT
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 / 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 ...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 / MIR / Resolution: 1.75 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 1.0Jun 26, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,4426
Polymers79,0652
Non-polymers3764
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.509, 97.408, 85.963
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 / DIHYDROXYACETONE KINASE


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


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


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.2 Å3/Da / Density % sol: 48.5 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
180 mMsodium acetate1reservoirpH5.0
2160 mMammonium sulfate1reservoir
317 %(w/v)PEG40001reservoir
415 %(w/v)MPD1reservoir
530 mg/mlprotein1drop
65 %(w/v)HEPES1droppH7.5
72 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 78957 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 19.4
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.172 / % possible all: 97.5
Reflection
*PLUS
Highest resolution: 1.75 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 97.5 % / Rmerge(I) obs: 0.172

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SHARPphasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MIR / Resolution: 1.75→24.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2157 2.7 %RANDOM
Rwork0.172 ---
obs0.172 76798 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--0.79 Å20 Å20 Å2
2--1.27 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 22 491 5555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9686954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7635664
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_restr0.1330.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.023880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.22640
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5570.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9862.53306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0963.55266
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6413.51812
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.494.51688
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
11324medium positional0.120.5
21189medium positional0.150.5
11324medium thermal1.132
21189medium thermal1.392
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.293 98
Rwork0.253 4630
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)
10.52440.0064-0.14510.02470.00430.77280.03250.047-0.007-0.016-0.02270.0035-0.0235-0.1048-0.00980.0090.0138-0.00880.045300.016363.3318.00458.591
20.4095-0.0527-0.2279-0.02530.09590.53110.0246-0.08340.0185-0.00510.0163-0.0079-0.03230.0913-0.04090.0104-0.0104-0.00160.0572-0.01680.0182101.29818.64670.319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 368
2X-RAY DIFFRACTION2B20 - 368
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.1715
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.618

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