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- PDB-3kz9: Crystal structure of the master transcriptional regulator, SmcR, ... -

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Basic information

Entry
Database: PDB / ID: 3kz9
TitleCrystal structure of the master transcriptional regulator, SmcR, in Vibrio vulnificus provides insight into its DNA recognition mechanism
ComponentsSmcR
KeywordsTRANSCRIPTION REGULATOR / Vibrio vulnificus / SmcR / Transcriptional regulator / Quorum sensing / DNA-binding / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
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
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKim, M.H. / Kim, Y. / Choi, W.-C. / Hwang, J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The crystal structure of SmcR, a quorum-sensing master regulator of Vibrio vulnificus, provides insight into its regulation of transcription
Authors: Kim, Y. / Kim, B.S. / Park, Y.J. / Choi, W.-C. / Hwang, J. / Kang, B.S. / Oh, T.-K. / Choi, S.H. / Kim, M.H.
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SmcR
B: SmcR
C: SmcR
D: SmcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,78310
Polymers96,2064
Non-polymers5766
Water8,161453
1
A: SmcR
B: SmcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2954
Polymers48,1032
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-18 kcal/mol
Surface area19570 Å2
MethodPISA
2
C: SmcR
D: SmcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4876
Polymers48,1032
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-17 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.494, 99.025, 129.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SmcR / SmcR-like protein / VvpR


Mass: 24051.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Plasmid: pHis-Parallel1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q9L8G8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Lithium sulfate, 7% PEG 3000, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 16, 2006
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. all: 59111 / Num. obs: 56004 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.072 / Rsym value: 0.047 / Net I/σ(I): 26.97
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.28 / Num. unique all: 5617 / Rsym value: 0.393 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.92 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 10.047 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.217 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: partially refined SeMet_SmcR model
RfactorNum. reflection% reflectionSelection details
Rfree0.25095 2979 5.1 %RANDOM
Rwork0.19759 ---
all0.212 59111 --
obs0.20033 56004 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å20 Å2
2--2.63 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 30 453 7043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226883
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9369361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2845838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81624.033362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.342151209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9111559
X-RAY DIFFRACTIONr_chiral_restr0.0920.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025283
X-RAY DIFFRACTIONr_nbd_refined0.2070.23395
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24801
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2416
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.235
X-RAY DIFFRACTIONr_mcbond_it0.9781.54270
X-RAY DIFFRACTIONr_mcangle_it1.48426725
X-RAY DIFFRACTIONr_scbond_it2.47132959
X-RAY DIFFRACTIONr_scangle_it3.6294.52636
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 193 -
Rwork0.212 3923 -
obs--94.93 %
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)
11.25140.7163-0.58480.6393-0.41770.8417-0.03680.0427-0.21060.0661-0.0619-0.12740.1604-0.00140.0987-0.01330.03130.037-0.0540.05720.036215.4834.87155.895
22.11330.20810.12860.53490.05290.0110.00790.1647-0.082-0.0213-0.0673-0.00490.0259-0.13130.0594-0.0306-0.00340.01260.05020.0146-0.07041.46549.86642.65
30.79280.3786-0.25990.7114-0.49960.35090.05190.0038-0.05320.0021-0.04960.00590.0844-0.0221-0.0023-0.018-0.02510.003-0.03390.0215-0.030833.73285.4257.161
42.11240.19720.16520.5584-0.08510.10280.02790.0170.0048-0.0146-0.03320.0413-0.0012-0.17840.0053-0.05690.0114-0.00610.04690.0241-0.097420.313100.66743.093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 205
2X-RAY DIFFRACTION2B0 - 202
3X-RAY DIFFRACTION3C3 - 205
4X-RAY DIFFRACTION4D5 - 203

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