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- PDB-1uoe: Crystal structure of the dihydroxyacetone kinase from E. coli in ... -

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Basic information

Entry
Database: PDB / ID: 1uoe
TitleCrystal structure of the dihydroxyacetone kinase from E. coli in complex with glyceraldehyde
ComponentsDIHYDROXYACETONE KINASE
KeywordsTRANSFERASE / KINASE
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 / pyruvate metabolic process / glycerol catabolic 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 / pyruvate metabolic process / glycerol catabolic 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSiebold, C. / Garcia-Alles, L.F. / Luthi-Nyffeler, T. / Flukiger-Bruhwiler, K. / Burgi, H.-B. / Baumann, U. / Erni, B.
CitationJournal: Biochemistry / Year: 2004
Title: Phosphoenolpyruvate- and ATP-Dependent Dihydroxyacetone Kinases: Covalent Substrate-Binding and Kinetic Mechanism
Authors: Garcia-Alles, L.F. / Siebold, C. / Luthi-Nyffeler, T. / Flukiger-Bruhwiler, K. / Schneider, P. / Burgi, H.-B. / Baumann, U. / Erni, B.
History
DepositionSep 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2004Provider: 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: DIHYDROXYACETONE KINASE
B: DIHYDROXYACETONE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4406
Polymers79,0632
Non-polymers3764
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.540, 97.315, 85.997
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
11GLNGLNCYSCYSAA20 - 20420 - 204
21GLNGLNCYSCYSBB20 - 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 DIHYDROXYACETONE KINASE


Mass: 39531.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENTLY MODIFIED HIS A230 AND B230 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / 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.: 478 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growpH: 5 / Details: pH 5.00

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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: 2→25 Å / Num. obs: 54971 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.1

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Processing

SoftwareName: REFMAC / Version: 5.1.19 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.157 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES A1 - A19 AND B1 - B19 ARE DISORDERED. LOOPS A205 - A217 AND B205 - B217 WERE ALS NOT VISIBLE IN THE ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1544 2.8 %RANDOM
Rwork0.178 ---
obs0.179 53425 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 parametersBiso mean: 17.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--2.23 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 22 478 5570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215121
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9676966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8155668
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_restr0.150.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.023880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.22647
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8092.53306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8443.55275
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5383.51815
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3914.51688
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
11323medium positional0.140.5
21188medium positional0.380.5
11323medium thermal1.472
21188medium thermal1.632
LS refinement shellResolution: 2→2.04 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.245 93
Rwork0.19 2939
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)
11.033-0.0036-0.27480.1517-0.10931.15970.05530.10160.0274-0.0177-0.00950.029-0.0548-0.233-0.04580.06050.0241-0.01070.06780.01050.068863.402218.081258.6264
20.89070.0189-0.37350.15140.13210.69240.0412-0.16780.07420.00150.0166-0.0489-0.05870.1721-0.05790.0712-0.0242-0.00040.0873-0.02890.0689101.392818.584870.351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 368
2X-RAY DIFFRACTION2B20 - 368

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