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- PDB-4mk6: Crystal Structure of Probable Dihydroxyacetone Kinase Regulator D... -

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Basic information

Entry
Database: PDB / ID: 4mk6
TitleCrystal Structure of Probable Dihydroxyacetone Kinase Regulator DHSK_reg from Listeria monocytogenes EGD-e
ComponentsProbable Dihydroxyacetone Kinase Regulator DHSK_reg
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Alpha-beta-fold / TetR-fold
Function / homology
Function and homology information


Transcriptional regulator TetR, C-terminal, Firmicutes type / Transcriptional regulator C-terminal region / Tetracycline Repressor, domain 2 / 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
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsKim, Y. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Probable Dihydroxyacetone Kinase Regulator DHSK_reg from Listeria monocytogenes EGD-e
Authors: Kim, Y. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable Dihydroxyacetone Kinase Regulator DHSK_reg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1533
Polymers22,0291
Non-polymers1242
Water59433
1
A: Probable Dihydroxyacetone Kinase Regulator DHSK_reg
hetero molecules

A: Probable Dihydroxyacetone Kinase Regulator DHSK_reg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3076
Polymers44,0582
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area3240 Å2
ΔGint-2 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.039, 77.039, 142.027
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-333-

HOH

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Components

#1: Protein Probable Dihydroxyacetone Kinase Regulator DHSK_reg


Mass: 22029.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0480 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8Y9P4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride, 0.1 M HEPES pH 7.5, 15 %(v/v) ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 10941 / Num. obs: 10941 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 57.8 Å2 / Rsym value: 0.074 / Net I/σ(I): 12.6
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 516 / Rsym value: 0.725 / % possible all: 98.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→30.193 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.24 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.232 523 4.79 %mixed
Rwork0.197 ---
all0.198 10929 --
obs0.198 10929 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.9 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 8 33 1565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031573
X-RAY DIFFRACTIONf_angle_d0.6172119
X-RAY DIFFRACTIONf_dihedral_angle_d14.391561
X-RAY DIFFRACTIONf_chiral_restr0.049231
X-RAY DIFFRACTIONf_plane_restr0.002268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3496-2.58590.27771430.25272504264799
2.5859-2.95980.25721200.226225652685100
2.9598-3.7280.23941250.208125922717100
3.728-30.19590.21611350.17842745288099
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)
15.9824-1.94192.24855.3714-2.26698.51990.3353-0.5087-1.0622-0.38180.14190.93360.9426-0.3351-0.50340.48860.006-0.08970.43590.19430.66175.105319.73223.5626
24.31644.9145-3.17385.6513-3.43882.8271-0.18090.6532-1.00150.63211.17071.43160.4009-1.2622-1.02140.7798-0.0105-0.07430.92220.40581.307623.096433.72591.7717
36.14520.79430.20544.85810.0833.29720.12230.00010.2567-0.07040.0835-0.129-0.38910.0116-0.23740.40490.05460.0090.30340.04610.251832.110927.61168.3506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 185 )

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