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- PDB-2a61: The crystal structure of transcriptional regulator Tm0710 from Th... -

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Basic information

Entry
Database: PDB / ID: 2a61
TitleThe crystal structure of transcriptional regulator Tm0710 from Thermotoga maritima
Componentstranscriptional regulator Tm0710
KeywordsTRANSCRIPTION / TM0710 / APC4350 / MCSG / Midwest Center for Structural Genomics / PSI / Protein structure Initiative / transcriptional regulator / MarR
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLunin, V.V. / Evdokimova, E. / Kudritska, M. / Chang, C. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of transcriptional regulator Tm0710 from Thermotoga maritima
Authors: Lunin, V.V. / Evdokimova, E. / Kudritska, M. / Chang, C. / Joachimiak, A. / Edwards, A. / Savchenko, A.
History
DepositionJul 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 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: transcriptional regulator Tm0710
B: transcriptional regulator Tm0710
C: transcriptional regulator Tm0710
D: transcriptional regulator Tm0710


Theoretical massNumber of molelcules
Total (without water)66,9624
Polymers66,9624
Non-polymers00
Water7,422412
1
A: transcriptional regulator Tm0710
B: transcriptional regulator Tm0710


Theoretical massNumber of molelcules
Total (without water)33,4812
Polymers33,4812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-50 kcal/mol
Surface area14630 Å2
MethodPISA
2
C: transcriptional regulator Tm0710
D: transcriptional regulator Tm0710


Theoretical massNumber of molelcules
Total (without water)33,4812
Polymers33,4812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-51 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.290, 50.380, 127.560
Angle α, β, γ (deg.)90.00, 96.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer, representated by chains (A,B) or (C,D)

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Components

#1: Protein
transcriptional regulator Tm0710


Mass: 16740.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: MODIFIED PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: GenBank: 15643473, UniProt: Q9WZG9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.5 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Mg Acetate, 0.1M Na Cacodylate pH 6.5, 20% PEG8K, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97932 / Wavelength: 0.97932 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 40215 / Num. obs: 40215 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.85 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.662 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27052 2145 5.1 %RANDOM
Rwork0.2097 ---
all0.21282 40215 --
obs0.21282 40215 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.757 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å2-0.47 Å2
2---2.18 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 0 412 5041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224705
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3922.0066299
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8965572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57922.632209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45215993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7031553
X-RAY DIFFRACTIONr_chiral_restr0.0960.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023413
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.22297
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23321
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2307
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0981.52934
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64724580
X-RAY DIFFRACTIONr_scbond_it2.80931949
X-RAY DIFFRACTIONr_scangle_it4.3854.51714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 17 -
Rwork0.249 357 -
obs--100 %

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