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- PDB-4kmr: Structure of a putative transcriptional regulator of LacI family ... -

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Basic information

Entry
Database: PDB / ID: 4kmr
TitleStructure of a putative transcriptional regulator of LacI family from Sanguibacter keddieii DSM 10542.
ComponentsTranscriptional regulator, LacI family
KeywordsTranscription regulator / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / LacI
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, LacI family
Similarity search - Component
Biological speciesSanguibacter keddieii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a putative transcriptional regulator of LacI family from Sanguibacter keddieii DSM 10542.
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9854
Polymers59,9382
Non-polymers472
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-25 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.175, 120.205, 44.962
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcriptional regulator, LacI family


Mass: 29968.912 Da / Num. of mol.: 2 / Fragment: C-terminal ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sanguibacter keddieii (bacteria) / Strain: DSM 10542 / Gene: Sked_03100 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1BJM2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FOLLOWING SEQUENCE WAS FOR THE PROTEIN EXPRESSED: ...THE FOLLOWING SEQUENCE WAS FOR THE PROTEIN EXPRESSED:MHHHHHHSSGVDLWSHPQFEKGTENLYFQSNAMATGPEGRAAPTLRDVAQVAGVSFKTVSNVLNDHPQVRPATRTKVLAAVEQVGYRPNLAARNLRLGRSGVIGLAVPELGQAFFAQLADEVIRVAAEQDLVVLVEQTGGLRERELEALRNPRLSLTDGLLLAPLGLTQDDVLPDPAGRPLVVLGEPLFPGPVDHVTMQHEAAARAATEHLLGLGRRRVMLLGAHATERTGVAALRYAGYREALTAAGLAVDDDLVVPVETWDRSSGAEAMARVLDAGVRMDAVFAMNDDLALGALRSLQERGVAVPGDVALMGFDDVADGRYTYPSLTTVEPGRHDIARAAVTMLSERIADAGTGAIEPRLTAPEFRLVVRESTGG. HOWEVER, THE PROTEIN UNDERWENT DEGRADATION OF THE PROTEIN DURING CRYSTALLIZATION SET UP. ITS KNOW THAT THE DNA-BINDING DOMAIN OF THIS LACI FAMILY OF TRANSCRIPTIONAL REGULATORS IS PRONE TO DEGRADATION.

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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: 35.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium Chloride, 0.1 M HEPES, 25% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2013 / Details: MIRROW
RadiationMonochromator: SI-CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 78844 / Num. obs: 78844 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 33.9
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3899 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.45→22.47 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.026 / SU ML: 0.038 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 3853 5 %RANDOM
Rwork0.1252 ---
obs0.12791 72986 97.38 %-
all-72986 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.13 Å2
2---0 Å20 Å2
3----0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.45→22.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 2 486 4481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194162
X-RAY DIFFRACTIONr_bond_other_d0.0010.024094
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9975671
X-RAY DIFFRACTIONr_angle_other_deg0.9139343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9755556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.05122.123179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57715613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5541554
X-RAY DIFFRACTIONr_chiral_restr0.1230.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214823
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02925
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr5.7134157
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded18.71454091
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 218 -
Rwork0.116 4239 -
obs--77.2 %
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)
10.86290.059-0.10520.99720.15451.69380.0434-0.05390.05890.0953-0.0240.0563-0.0341-0.0369-0.01940.0127-0.00560.00580.01040.00260.015642.613325.879652.6325
21.7624-0.50672.19970.6183-0.51022.9471-0.1233-0.02830.06250.09060.0356-0.0097-0.2014-0.03270.08770.03820.0033-0.00760.01780.010.027643.268338.777842.9852
30.436-0.2212-0.05510.9934-0.26120.3979-0.03960.0108-0.01970.06740.01320.0825-0.0316-0.02880.02640.01-0.0008-0.00340.00460.00320.028224.657837.365331.9062
41.38420.20961.03170.25050.02761.39850.05990.09990.0130.008-0.0686-0.03310.06220.19620.00870.00540.0064-0.00550.04880.01280.019848.032632.114239.7425
50.98820.07710.33110.71820.66021.22970.04710.0094-0.11340.077-0.0149-0.04210.126-0.0517-0.03220.0404-0.0205-0.01220.01420.00130.018539.62799.399949.0503
65.87760.09981.83513.7295-0.95874.84680.20490.2301-0.12090.1397-0.1418-0.16940.02870.1989-0.06320.0257-0.0059-0.02480.02810.01790.039638.3623-1.800452.7206
70.60490.2437-0.08990.45270.08920.3798-0.02530.0345-0.0577-0.05450.0192-0.00710.0207-0.00380.00610.02040.0018-0.0090.0039-0.00630.013420.62934.82430.5576
80.9789-0.25170.79210.8155-0.61981.12390.0473-0.1442-0.07630.0832-0.0306-0.0313-0.0209-0.0513-0.01670.0158-0.0132-0.01210.03780.01410.012227.49254.431554.0195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A66 - 147
2X-RAY DIFFRACTION2A148 - 177
3X-RAY DIFFRACTION3A178 - 303
4X-RAY DIFFRACTION4A304 - 345
5X-RAY DIFFRACTION5B68 - 138
6X-RAY DIFFRACTION6B145 - 164
7X-RAY DIFFRACTION7B165 - 303
8X-RAY DIFFRACTION8B304 - 345

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