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- PDB-2iu5: Dihydroxyacetone kinase operon activator DhaS -

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Basic information

Entry
Database: PDB / ID: 2iu5
TitleDihydroxyacetone kinase operon activator DhaS
ComponentsHTH-TYPE DHAKLM OPERON TRANSCRIPTIONAL ACTIVATOR DHAS
KeywordsTRANSCRIPTION / SYNTHASE / ACTIVATOR / TETR FAMILY
Function / homology
Function and homology information


Transcription regulator DhaS / Transcriptional regulator TetR, C-terminal, Firmicutes type / Transcriptional regulator C-terminal region / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...Transcription regulator DhaS / Transcriptional regulator TetR, C-terminal, Firmicutes type / Transcriptional regulator C-terminal region / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type dhaKLM operon transcriptional activator DhaS
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS SUBSP. LACTIS IL1403 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.6 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 1.2May 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: HTH-TYPE DHAKLM OPERON TRANSCRIPTIONAL ACTIVATOR DHAS
B: HTH-TYPE DHAKLM OPERON TRANSCRIPTIONAL ACTIVATOR DHAS


Theoretical massNumber of molelcules
Total (without water)47,1502
Polymers47,1502
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-18 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.459, 46.284, 171.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 3 / Auth seq-ID: 4 - 179 / Label seq-ID: 11 - 186

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein HTH-TYPE DHAKLM OPERON TRANSCRIPTIONAL ACTIVATOR DHAS / DHAS / YCEG


Mass: 23574.805 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS SUBSP. LACTIS IL1403 (lactic acid bacteria)
Description: NESTLE / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CIV9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 9 TO GLU ENGINEERED RESIDUE IN CHAIN B, LYS 9 TO GLU
Sequence detailsSECOND AMINO ACID IS MODIFIED TO GLUTAMATE FROM LYSINE AND THE C-TERMINAL HAS EIGHT ADDITIONAL ...SECOND AMINO ACID IS MODIFIED TO GLUTAMATE FROM LYSINE AND THE C-TERMINAL HAS EIGHT ADDITIONAL AMINOACIDS NAMELY LEUCINE AND GLUTAMATE FOLLOWED BY A HEXA-HIS TAG

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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: 1.9 Å3/Da / Density % sol: 34.64 %
Crystal growpH: 6
Details: THE CONCENTRATED PROTEIN (20 MG/ML) WAS MIXED WITH BUFFER CONTAINING 50 MM NA-CACODYLATE PH 6.0, 1.7 M AMMONIUM SULFATE, 0.015 M MG-ACETATE IN A 1:1 RATIO.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 45492 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 4.01 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 0.07 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.502 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2013 4.2 %RANDOM
Rwork0.195 ---
obs0.197 45492 99.3 %-
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: 23.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2--0.9 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 0 294 3328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9314183
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7515354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07625.2175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3815578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3491512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022354
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21572
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.22236
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2192
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3133.51803
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90132874
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.60141467
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0325.51309
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
704tight positional0.550.05
796loose positional1.075
704tight thermal1.520.5
796loose thermal2.8410
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 105
Rwork0.21 3352
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)
11.29780.799-1.05040.7674-0.81781.32130.03170.03710.0427-0.00780.0170.036-0.07720.0145-0.0487-0.10560.0061-0.0065-0.1496-0.0045-0.10812.93934.04437.11
20.89020.21130.47870.47630.27511.45480.048-0.002-0.0953-0.03870.0392-0.02320.08160.0512-0.08720.02280.0080.00520.0201-0.00460.010424.0229.23710.332
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 179
2X-RAY DIFFRACTION2B4 - 179

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