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- PDB-4hku: The crystal structure of TetR transcriptional regulator (lmo2814)... -

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Basic information

Entry
Database: PDB / ID: 4hku
TitleThe crystal structure of TetR transcriptional regulator (lmo2814) from Listeria monocytogenes EGD-e
ComponentsTetR transcriptional regulator
KeywordsTRANSCRIPTION / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain 27 / Tetracyclin repressor-like, C-terminal domain / 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 / MAD / Resolution: 2.302 Å
AuthorsTan, K. / Mack, J.C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of TetR transcriptional regulator (lmo2814) from Listeria monocytogenes EGD-e
Authors: Tan, K. / Mack, J.C. / Endres, M. / Joachimiak, A.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TetR transcriptional regulator
B: TetR transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)42,5172
Polymers42,5172
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-12 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.668, 81.560, 105.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe molecule is predicted to form a dimer.

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Components

#1: Protein TetR transcriptional regulator / Lmo2814 protein


Mass: 21258.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo2814 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pGrow7-K / References: UniProt: Q8Y3M1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium Acetate, 0.1M HEPES:NaOH, 20%(w/v) PEG3000, pH 7.5, 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: 0.97926, 0.97951
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2012 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979511
ReflectionResolution: 2.3→31 Å / Num. all: 18258 / Num. obs: 18258 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 43.23 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 26.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.4 / Num. unique all: 899 / % possible all: 98.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.302→30.708 Å / SU ML: 0.69 / σ(F): 1.34 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 932 5.13 %random
Rwork0.1945 ---
obs0.1976 18174 98.4 %-
all-18174 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.89 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9945 Å20 Å2-0 Å2
2--9.9094 Å20 Å2
3----10.9039 Å2
Refinement stepCycle: LAST / Resolution: 2.302→30.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2878 0 0 54 2932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082950
X-RAY DIFFRACTIONf_angle_d0.9994006
X-RAY DIFFRACTIONf_dihedral_angle_d17.6061052
X-RAY DIFFRACTIONf_chiral_restr0.071431
X-RAY DIFFRACTIONf_plane_restr0.004509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3024-2.42370.29351310.22362336X-RAY DIFFRACTION95
2.4237-2.57550.33551340.23132409X-RAY DIFFRACTION98
2.5755-2.77420.30791250.23182425X-RAY DIFFRACTION99
2.7742-3.05320.32811340.23982445X-RAY DIFFRACTION99
3.0532-3.49450.29071380.21552476X-RAY DIFFRACTION99
3.4945-4.40060.2431400.17912511X-RAY DIFFRACTION100
4.4006-30.71060.2011300.16652640X-RAY DIFFRACTION99
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)
18.6301-0.985-3.21734.95121.62974.6639-0.06990.2042-0.35820.1991-0.0098-0.2515-0.0452-0.31340.1180.28260.06860.01120.26560.040.32647.1098-20.47792.1351
27.4418-3.2499-2.35367.2245.44674.15240.40970.48460.259-0.0441-0.0352-0.7643-0.29220.5343-0.46080.3024-0.0784-0.01920.47910.06360.302155.7558-16.9903-2.5624
37.5728-5.9902-4.47536.82574.78744.99790.61050.86160.368-0.417-0.6782-0.1163-0.5169-0.37160.11560.40670.03380.03910.27740.04980.322740.5106-7.02255.5932
43.9714-3.952-1.80938.4341.78832.41090.23820.3406-0.0617-0.649-0.39570.6619-0.3001-0.79380.11150.34640.0303-0.06760.5003-0.08140.294923.02141.782211.4807
57.0691-1.1184-0.75139.13232.3183.5486-0.3204-0.1083-0.40120.35770.0084-0.24280.32340.1710.07730.41070.06940.01150.49740.01210.216139.925-11.371914.3946
65.1186-3.9639-0.8116.98380.72524.02870.0039-0.27410.4120.09770.1563-0.5414-0.14020.8955-0.14090.38490.0276-0.0090.4475-0.09030.251734.1714.796116.3301
76.6871-0.0652-2.4539.1229-1.21858.397-0.1214-0.183-0.3686-0.109-0.53270.67730.913-0.56180.4160.3478-0.01310.10080.5848-0.07960.298421.7641.40524.0054
84.4714-0.6720.12233.16241.06235.84090.104-0.1512-1.11570.1202-0.0383-0.34131.57960.7005-0.20150.88290.3102-0.01310.4959-0.01170.685447.7171-21.150849.4735
93.9819-3.6475-0.893.49070.47470.7608-0.0007-0.1328-0.14010.4369-0.1868-0.3410.10160.38840.25770.53910.1024-0.07170.5625-0.03170.274637.9126-0.204345.318
103.644-1.93590.16456.6878-0.26073.73460.0076-0.07160.0079-0.1058-0.0338-0.2910.27850.59880.06310.27850.0122-0.02980.426-0.06780.166136.70574.039833.8649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:34)
2X-RAY DIFFRACTION2chain 'A' and (resseq 35:47)
3X-RAY DIFFRACTION3chain 'A' and (resseq 48:68)
4X-RAY DIFFRACTION4chain 'A' and (resseq 69:99)
5X-RAY DIFFRACTION5chain 'A' and (resseq 100:114)
6X-RAY DIFFRACTION6chain 'A' and (resseq 115:157)
7X-RAY DIFFRACTION7chain 'A' and (resseq 158:175)
8X-RAY DIFFRACTION8chain 'B' and (resseq 3:47)
9X-RAY DIFFRACTION9chain 'B' and (resseq 48:77)
10X-RAY DIFFRACTION10chain 'B' and (resseq 78:175)

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