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- PDB-2iu6: REGULATION OF THE DHA OPERON OF LACTOCOCCUS LACTIS -

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Basic information

Entry
Database: PDB / ID: 2iu6
TitleREGULATION OF THE DHA OPERON OF LACTOCOCCUS LACTIS
ComponentsDIHYDROXYACETONE KINASE
KeywordsTRANSFERASE / KINASE / DIHYDROXYACETONE KINASE TRANSFERASE
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _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 / _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)74,8804
Polymers74,6952
Non-polymers1842
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.090, 101.090, 148.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEALAALAAA3 - 1883 - 188
21PHEPHEALAALABB3 - 1883 - 188
12TYRTYRHISHISAA220 - 335220 - 335
22TYRTYRHISHISBB220 - 335220 - 335

NCS ensembles :
ID
1
2

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Components

#1: Protein DIHYDROXYACETONE KINASE / DHAQ


Mass: 37347.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Strain: IL1403 / Description: NESTLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CIW0, glucokinase
#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.: 278 / Source method: isolated from a natural source / Formula: H2O
Sequence details13 ADDITIONAL N-TERMINAL AMINO ACIDS THAT OCCUR NATURALLY INCLUDED NAMELY MEFYNSTNEIPEE. THE ...13 ADDITIONAL N-TERMINAL AMINO ACIDS 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: 2.97 Å3/Da / Density % sol: 58.26 %
Crystal growpH: 7 / Details: 0.15 M DL-MALIC ACID PH 7.0, 20% PEG-3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS-IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 59910 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 12.38 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.6
Reflection shellResolution: 2→2.04 Å / Redundancy: 10.95 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 6.88 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OI2

1oi2


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.286 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1497 2.5 %RANDOM
Rwork0.173 ---
obs0.173 58399 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: 30.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0.54 Å20 Å2
2---1.08 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4981 0 12 278 5271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9676898
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27524.795219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31815886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.7491516
X-RAY DIFFRACTIONr_chiral_restr0.290.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.023796
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.22366
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23518
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4543.53240
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82335073
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68242112
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9385.51825
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
1744tight positional0.140.05
2463tight positional0.150.05
1687loose positional0.525
2475loose positional0.365
1744tight thermal0.630.5
2463tight thermal0.730.5
1687loose thermal2.0110
2475loose thermal2.6710
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.245 109
Rwork0.212 4257
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)
13.85750.32240.69311.86090.28991.48420.09930.1611-0.733-0.00670.0826-0.23490.426-0.0555-0.1819-0.0135-0.0414-0.0424-0.0633-0.0563-0.006481.17523.6498.79
23.09670.4244-0.2560.81480.15361.47050.0215-0.09730.1369-0.004-0.02980.0012-0.0812-0.00130.0082-0.19170.0161-0.0078-0.11010.009-0.225186.68849.72623.14
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 189
2X-RAY DIFFRACTION1A210 - 335
3X-RAY DIFFRACTION2B2 - 189
4X-RAY DIFFRACTION2B210 - 335

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