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- PDB-1zlj: Crystal Structure of the Mycobacterium tuberculosis Hypoxic Respo... -

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Basic information

Entry
Database: PDB / ID: 1zlj
TitleCrystal Structure of the Mycobacterium tuberculosis Hypoxic Response Regulator DosR C-terminal Domain
ComponentsDormancy Survival Regulator
KeywordsTRANSCRIPTION / helix-turn-helix
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Two component transcriptional regulatoryprotein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWisedchaisri, G. / Wu, M. / Rice, A.E. / Roberts, D.M. / Sherman, D.R. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structures of Mycobacterium tuberculosis DosR and DosR-DNA complex involved in gene activation during adaptation to hypoxic latency.
Authors: Wisedchaisri, G. / Wu, M. / Rice, A.E. / Roberts, D.M. / Sherman, D.R. / Hol, W.G.J.
History
DepositionMay 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: 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: Dormancy Survival Regulator
B: Dormancy Survival Regulator
C: Dormancy Survival Regulator
D: Dormancy Survival Regulator
E: Dormancy Survival Regulator
F: Dormancy Survival Regulator
G: Dormancy Survival Regulator
H: Dormancy Survival Regulator


Theoretical massNumber of molelcules
Total (without water)70,1258
Polymers70,1258
Non-polymers00
Water3,531196
1
A: Dormancy Survival Regulator
B: Dormancy Survival Regulator


Theoretical massNumber of molelcules
Total (without water)17,5312
Polymers17,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Dormancy Survival Regulator
D: Dormancy Survival Regulator


Theoretical massNumber of molelcules
Total (without water)17,5312
Polymers17,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Dormancy Survival Regulator
F: Dormancy Survival Regulator


Theoretical massNumber of molelcules
Total (without water)17,5312
Polymers17,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Dormancy Survival Regulator
H: Dormancy Survival Regulator


Theoretical massNumber of molelcules
Total (without water)17,5312
Polymers17,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.069, 60.488, 74.226
Angle α, β, γ (deg.)89.90, 89.91, 90.99
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPPROAA145 - 2136 - 74
21ASPPROEE145 - 2136 - 74
12SERARGBB141 - 2092 - 70
22SERARGFF141 - 2092 - 70
13ASPPROCC145 - 2136 - 74
23ASPPROGG145 - 2136 - 74
14GLNARGDD144 - 2095 - 70
24GLNARGHH144 - 2095 - 70

NCS ensembles :
ID
1
2
3
4
DetailsThe asymmetric unit contains 8 biological monomers forming 4 functional dimers.

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Components

#1: Protein
Dormancy Survival Regulator / DosR


Mass: 8765.596 Da / Num. of mol.: 8 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dosR, devR, Rv3133c / Plasmid: pET28(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 15610269, UniProt: R4MI41*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.15 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 5000mme, ammonium sulfate, sodium chloride, MES, glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2004
RadiationMonochromator: KOHZU: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 37716 / % possible obs: 97.3 % / Observed criterion σ(I): 3.7 / Redundancy: 7.48 % / Biso Wilson estimate: 26.35 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.7 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.875 / SU ML: 0.11 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1894 5 %RANDOM
Rwork0.186 ---
obs0.188 35816 96.6 %-
all-39046 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20.07 Å2-0.15 Å2
2---1.9 Å2-0.2 Å2
3---2.37 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 0 196 4414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224252
X-RAY DIFFRACTIONr_bond_other_d0.0010.024130
X-RAY DIFFRACTIONr_angle_refined_deg1.31825716
X-RAY DIFFRACTIONr_angle_other_deg0.74239554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2945538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02814
X-RAY DIFFRACTIONr_nbd_refined0.2230.3979
X-RAY DIFFRACTIONr_nbd_other0.2490.34637
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0950.52747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5218
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.332
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.3194
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.30722706
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.19934326
X-RAY DIFFRACTIONr_scbond_it1.59621546
X-RAY DIFFRACTIONr_scangle_it2.68631390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A390tight positional0.020.05
2B406tight positional0.020.05
3C408tight positional0.020.05
4D406tight positional0.020.05
1A616medium positional0.420.5
2B647medium positional0.410.5
3C654medium positional0.370.5
4D647medium positional0.540.5
1A390tight thermal0.130.5
2B406tight thermal0.110.5
3C408tight thermal0.120.5
4D406tight thermal0.110.5
1A616medium thermal0.272
2B647medium thermal0.342
3C654medium thermal0.32
4D647medium thermal0.332
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 126 -
Rwork0.216 2214 -
obs--80.58 %

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