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- PDB-2guh: Crystal Structure of the Putative TetR-family Transcriptional Reg... -

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Basic information

Entry
Database: PDB / ID: 2guh
TitleCrystal Structure of the Putative TetR-family Transcriptional Regulator from Rhodococcus sp. RHA1
ComponentsPutative TetR-family transcriptional regulator
KeywordsTRANSCRIPTION / helix-turn-helix / tetR fold / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Tetracyclin repressor-like, C-terminal domain 16 / Tetracyclin repressor-like, C-terminal domain / 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
Probable transcriptional regulator
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsKim, Y. / Joachimiak, A. / Skarina, T. / Zheng, H. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative TetR-family Transcriptional Regulator from Rhodococcus sp. RHA1
Authors: Kim, Y. / Joachimiak, A. / Skarina, T. / Zheng, H. / Edwards, A. / Savchenko, A.
History
DepositionApr 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database at the time ...SEQUENCE The sequence of the protein has not been deposited into any sequence database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative TetR-family transcriptional regulator
B: Putative TetR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3339
Polymers48,0122
Non-polymers3217
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-47 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.259, 72.130, 133.875
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 Putative TetR-family transcriptional regulator


Mass: 24005.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: rha6424 / Plasmid: modified pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q0S8Y3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25 % PEG3350, 0.2M MgCl2, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97872 Å
DetectorType: SBC-3 / Detector: CCD / Date: Apr 20, 2006 / Details: mirror
RadiationMonochromator: double crystal monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.52→23.37 Å / Num. all: 64582 / Num. obs: 63688 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.6
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3100 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
RESOLVEphasing
SHELXEmodel building
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→23.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.175 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18781 6421 10.1 %RANDOM
Rwork0.1685 ---
all0.17045 57196 --
obs0.17045 57196 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.302 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.52→23.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 19 450 3222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223194
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9924340
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1525427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96422.313147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87315585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9011542
X-RAY DIFFRACTIONr_chiral_restr0.0870.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022514
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.21837
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2372
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.263
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8741.52007
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48823252
X-RAY DIFFRACTIONr_scbond_it2.17931187
X-RAY DIFFRACTIONr_scangle_it3.324.51088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.519→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.229 437
Rwork0.195 4093
obs-4093
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)
10.7271-0.01330.03340.96820.17180.77670.02460.0798-0.0735-0.14640.00630.08570.06-0.0636-0.0309-0.01380.0003-0.0177-0.0204-0.0039-0.010337.89817.16521.918
20.88970.23260.09011.08530.04581.0769-0.02650.07910.0443-0.1180.0169-0.1135-0.12410.11240.0096-0.0307-0.00710.0013-0.03860.0039-0.025651.21935.18624.711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 19135 - 213
2X-RAY DIFFRACTION2BB14 - 19136 - 213

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