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- PDB-3kkc: The crystal structure OF TetR transcriptional regulator from Stre... -

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Basic information

Entry
Database: PDB / ID: 3kkc
TitleThe crystal structure OF TetR transcriptional regulator from Streptococcus agalactiae 2603V
ComponentsTetR family Transcriptional regulator
Keywordstranscription regulator / APC20805 / TetR / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / DNA-binding / Transcription / Transcription regulation
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
IMIDAZOLE / NICKEL (II) ION / Transcriptional regulator, TetR family / TetR family transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus agalactiae 2603V/R (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsTan, K. / Hatzos, C. / Morgan, T. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure OF TetR transcriptional regulator from Streptococcus agalactiae 2603V
Authors: Tan, K. / Hatzos, C. / Morgan, T. / Clancy, S. / Joachimiak, A.
History
DepositionNov 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TetR family Transcriptional regulator
B: TetR family Transcriptional regulator
C: TetR family Transcriptional regulator
D: TetR family Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,96020
Polymers85,8964
Non-polymers1,06416
Water543
1
A: TetR family Transcriptional regulator
B: TetR family Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,48010
Polymers42,9482
Non-polymers5328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-20 kcal/mol
Surface area18330 Å2
MethodPISA
2
C: TetR family Transcriptional regulator
D: TetR family Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,48010
Polymers42,9482
Non-polymers5328
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-18 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.351, 128.681, 74.566
Angle α, β, γ (deg.)90.00, 103.23, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. The chaisn A and B, C and D are predicted to form dimers, respectively.

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Components

#1: Protein
TetR family Transcriptional regulator


Mass: 21474.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae 2603V/R (bacteria)
Strain: 2603V / Gene: SAG0431, Streptococcus agalactiae / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q8E1C6, UniProt: Q9F8C4*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M Tri-sodium citrate dihydrate, 20% w/v PEG3350, 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: 0.97940, 0.97951
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979511
ReflectionResolution: 2.5→48.2 Å / Num. all: 27427 / Num. obs: 27427 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 24.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.44 / Num. unique all: 1154 / % possible all: 83.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→48.148 Å / SU ML: 0.4 / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2788 2665 5.02 %random
Rwork0.208 ---
all0.2119 53071 --
obs0.2119 53071 95.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.513 Å2 / ksol: 0.297 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→48.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 64 3 6079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096208
X-RAY DIFFRACTIONf_angle_d1.2118360
X-RAY DIFFRACTIONf_dihedral_angle_d22.4812260
X-RAY DIFFRACTIONf_chiral_restr0.08918
X-RAY DIFFRACTIONf_plane_restr0.0041054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4991-2.58840.43142270.34674085X-RAY DIFFRACTION77
2.5884-2.69210.41522210.33814825X-RAY DIFFRACTION92
2.6921-2.81460.39372460.31035164X-RAY DIFFRACTION98
2.8146-2.96290.34142730.28225300X-RAY DIFFRACTION99
2.9629-3.14850.3592790.27565275X-RAY DIFFRACTION100
3.1485-3.39160.32222880.24685258X-RAY DIFFRACTION100
3.3916-3.73280.31792970.20555221X-RAY DIFFRACTION100
3.7328-4.27260.242840.17015245X-RAY DIFFRACTION100
4.2726-5.38190.23292780.14595190X-RAY DIFFRACTION98
5.3819-48.1570.23792720.18984843X-RAY DIFFRACTION92
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.2321-0.6947-1.32822.80172.03792.3942-0.2379-0.286-0.74311.41560.3154-0.7361.11440.0814-0.25050.9088-0.0725-0.48740.57790.16660.958612.615556.683860.7904
22.0752-0.03140.7572.92490.18852.02790.01210.0950.32960.42750.07390.0021-0.2044-0.019-0.09520.58830.05630.01190.50120.10520.461
32.9904-1.88072.25812.6920.13122.14420.0281-0.27750.2655-0.43610.09840.0104-0.0774-0.3794-0.20130.6266-0.05220.03060.56630.01020.4767
42.7690.3721.76072.55920.73812.98670.01330.1787-0.1553-0.2556-0.02980.18760.39010.01880.0290.24170.08480.11060.4341-0.10030.3656
51.0513-0.61060.96153.5387-1.22621.4404-0.2101-1.46350.25891.0930.75-0.9302-0.358-0.5537-0.3560.62970.0083-0.03141.0088-0.24010.5481
63.35970.23421.74191.88561.69693.7283-0.10250.1605-0.0538-0.6294-0.06880.40180.071-0.01540.18390.69450.0327-0.15630.3693-0.10530.6369
71.4830.76931.8354.92340.89542.7139-0.37910.5916-0.3740.59471.2343-0.72570.33121.3433-0.72710.51960.0194-0.14790.794-0.01490.9898
81.3829-2.69621.27263.1972.00152.4520.1081-0.10960.1854-0.9119-0.20780.6181-0.9058-0.33490.19220.90230.0889-0.15480.5446-0.11390.7433
Refinement TLS groupSelection details: chain D resid 52:174

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