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- PDB-2iu4: Dihydroxyacetone kinase operon co-activator Dha-DhaQ -

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Basic information

Entry
Database: PDB / ID: 2iu4
TitleDihydroxyacetone kinase operon co-activator Dha-DhaQ
ComponentsDIHYDROXYACETONE KINASE
KeywordsTRANSFERASE / LACTOCOCCUS LACTIS / DIHYDROXYACETONE / CO-ACTIVATOR / KINASE
Function / homology
Function and homology information


glycerone kinase activity / glycerol catabolic process / cytosol
Similarity search - Function
Dihydroxyacetone kinase DhaK, subunit 1b / 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 1b / 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
DhaKLM operon coactivator DhaQ
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSrinivas, A. / Christen, S. / Baumann, U. / Erni, B.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Regulation of the Dha Operon of Lactococcus Lactis: A Deviation from the Rule Followed by the Tetr Family of Transcription Regulators
Authors: Christen, S. / Srinivas, A. / Bahler, P. / Zeller, A. / Pridmore, D. / Bieniossek, C. / Baumann, U. / Erni, B.
History
DepositionMay 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / 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_site
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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: DIHYDROXYACETONE KINASE
B: DIHYDROXYACETONE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2586
Polymers74,8732
Non-polymers3844
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.897, 99.897, 188.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A7 - 332
2113B7 - 332

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Components

#1: Protein DIHYDROXYACETONE KINASE / DHA-DHAQ


Mass: 37436.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9CIW0, glucokinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details13 ADDITIONAL N-TERMINAL AMINOACIDS THAT OCCUR NATURALLY INCLUDED NAMELY MEFYNSTNEIPEE. THE PROTEIN ...13 ADDITIONAL N-TERMINAL AMINOACIDS THAT OCCUR NATURALLY INCLUDED NAMELY MEFYNSTNEIPEE. THE PROTEIN IS C-TERMINAL HEXA-HIS TAGGED

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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: 3.54 Å3/Da / Density % sol: 65 %
Crystal growpH: 4.5
Details: 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.5, 2 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2154
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2154 Å / Relative weight: 1
ReflectionResolution: 1.96→40 Å / Num. obs: 77167 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.39 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.17
Reflection shellResolution: 1.96→2.04 Å / Redundancy: 4.54 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.66 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.71 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1583 2 %RANDOM
Rwork0.181 ---
obs0.182 76689 99.9 %-
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: 29.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5125 0 20 338 5483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225261
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9797131
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3095654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14224.887221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0315907
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.1841516
X-RAY DIFFRACTIONr_chiral_restr0.2010.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023911
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.22708
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.23705
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2375
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3950.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3633.53319
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75235232
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68242178
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9495.51897
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 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1295tight positional0.090.05
1234loose positional0.535
1295tight thermal0.440.5
1234loose thermal1.6610
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 71
Rwork0.19 5181
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)
10.55490.4780.00272.32680.47971.35870.0295-0.0781-0.06040.0045-0.0064-0.07640.0750.009-0.0231-0.1709-0.0549-0.007-0.13560.003-0.1144-44.34117.05317.934
21.58810.90820.16931.6299-0.19711.33510.02060.0051-0.0699-0.07820.0013-0.03820.06810.0146-0.0219-0.1045-0.0292-0.0181-0.2141-0.0062-0.1266-46.43216.652-12
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 332
2X-RAY DIFFRACTION2B7 - 332

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