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- PDB-2qko: Crystal structure of transcriptional regulator RHA06399 from Rhod... -

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Basic information

Entry
Database: PDB / ID: 2qko
TitleCrystal structure of transcriptional regulator RHA06399 from Rhodococcus sp. RHA1
ComponentsPossible transcriptional regulator, TetR family protein
KeywordsTRANSCRIPTION / Rhodococcus sp. / tetR family protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Tetracyclin repressor-like, C-terminal, group 31 / 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
Possible transcriptional regulator, TetR family protein
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsChang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of tetR family protein.
Authors: Chang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Possible transcriptional regulator, TetR family protein
B: Possible transcriptional regulator, TetR family protein
C: Possible transcriptional regulator, TetR family protein
D: Possible transcriptional regulator, TetR family protein


Theoretical massNumber of molelcules
Total (without water)96,8744
Polymers96,8744
Non-polymers00
Water1,74797
1
A: Possible transcriptional regulator, TetR family protein
B: Possible transcriptional regulator, TetR family protein


Theoretical massNumber of molelcules
Total (without water)48,4372
Polymers48,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-27 kcal/mol
Surface area16360 Å2
MethodPISA
2
C: Possible transcriptional regulator, TetR family protein
D: Possible transcriptional regulator, TetR family protein


Theoretical massNumber of molelcules
Total (without water)48,4372
Polymers48,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-26 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.307, 62.307, 164.243
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Possible transcriptional regulator, TetR family protein


Mass: 24218.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: RHA1_ro04181 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q0S912
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.9 Å3/Da / Density % sol: 35.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1M Bis-tris, 2.5M Ammonium sulfate, 1,5-Diaminopentane di-HCl, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 29754 / Num. obs: 29688 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 47.92 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 41.24
Reflection shellResolution: 2.35→2.37 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4.29 / Num. unique all: 752 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→38.43 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.227 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.524 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2733 1502 5.1 %RANDOM
Rwork0.23307 ---
all0.23513 28135 --
obs0.23513 28135 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.047 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.35→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5383 0 0 97 5480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225451
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9837404
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1955694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19322.441254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23615897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5161572
X-RAY DIFFRACTIONr_chiral_restr0.0680.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22577
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.23834
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7941.53607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23325575
X-RAY DIFFRACTIONr_scbond_it1.94432042
X-RAY DIFFRACTIONr_scangle_it2.9874.51829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 98 -
Rwork0.24 2086 -
obs-2184 100 %
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)
10.86622.50571.089418.32187.16748.4188-0.0591-0.15240.0102-1.6201-0.59340.9245-2.23-1.06480.65260.31440.4814-0.1476-0.0608-0.0403-0.16757.73616.204652.3369
21.47570.2259-0.68590.1807-0.29011.1273-0.02760.0928-0.2584-0.1026-0.12640.0984-0.0581-0.24690.154-0.05970.06690.04010.0211-0.0641-0.03717.0824-11.355456.6124
312.14858.6159-6.04467.413-4.26478.79130.2641-1.5028-0.92580.0431-1.0075-0.6122-0.17462.64860.7434-0.39420.0518-0.06140.73260.1854-0.14233.1765-8.179360.4436
40.2746-0.522-0.07941.31360.63080.8422-0.0761-0.1713-0.20660.0233-0.05870.19280.14890.17990.1348-0.06060.06470.0750.0337-0.0048-0.043817.7933-17.539456.2412
50.2394-1.8010.705619.9812-7.60459.5089-0.00830.1243-0.03271.674-0.6899-1.3128-2.46081.13420.69830.3569-0.5137-0.1876-0.05850.0516-0.153-7.47586.661987.8636
61.5247-0.2622-0.62760.28650.21291.0333-0.0241-0.0667-0.23970.1038-0.1451-0.1092-0.07970.22850.1692-0.0538-0.06420.04420.02490.0658-0.057-7.0675-11.343583.6146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 99
2X-RAY DIFFRACTION2A100 - 193
3X-RAY DIFFRACTION3B3 - 99
4X-RAY DIFFRACTION4B100 - 193
5X-RAY DIFFRACTION5D3 - 99
6X-RAY DIFFRACTION6D100 - 193

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