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- PDB-3r0j: Structure of PhoP from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3r0j
TitleStructure of PhoP from Mycobacterium tuberculosis
ComponentsPOSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP
KeywordsDNA BINDING PROTEIN / beta-alpha fold / winged helix-turn-helix / transcription regulator / DNA binding
Function / homology
Function and homology information


protein secretion by the type VII secretion system / glycolipid biosynthetic process / phosphorelay response regulator activity / positive regulation of lipid biosynthetic process / protein-DNA complex / response to oxidative stress / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription ...protein secretion by the type VII secretion system / glycolipid biosynthetic process / phosphorelay response regulator activity / positive regulation of lipid biosynthetic process / protein-DNA complex / response to oxidative stress / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / metal ion binding / plasma membrane / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / 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. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / 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 / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
R-1,2-PROPANEDIOL / Possible two component system response transcriptional positive regulator PhoP
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsMenon, S. / Wang, S.
CitationJournal: Biochemistry / Year: 2011
Title: Structure of the Response Regulator PhoP from Mycobacterium tuberculosis Reveals a Dimer through the Receiver Domain.
Authors: Menon, S. / Wang, S.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP
B: POSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6578
Polymers56,1012
Non-polymers5566
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.228, 138.242, 58.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A19 - 84
2113B19 - 84
1213A86 - 139
2213B86 - 139
1123A151 - 225
2123B151 - 225
1223A230 - 243
2223B230 - 243

NCS ensembles :
ID
1
2

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Components

#1: Protein POSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP


Mass: 28050.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: phoP, Rv0757 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P71814
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.8 M ammonium sulfate, 1.5% PEG 400, 12% 1.2-propanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9804, 0.9800, 0.9537
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 12, 2010
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98041
20.981
30.95371
ReflectionResolution: 2.5→30 Å / Num. all: 22929 / Num. obs: 22929 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 16.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.78 / Num. unique all: 1104 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.81 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.929 / SU ML: 0.178 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24515 1157 5.1 %RANDOM
Rwork0.21174 ---
obs0.21344 21622 98.57 %-
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: 60.796 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å20 Å20 Å2
2--3.32 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 30 78 3622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223598
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9884879
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6285441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36522.606165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95215.049617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3331540
X-RAY DIFFRACTIONr_chiral_restr0.1070.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212682
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7561.52205
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45823562
X-RAY DIFFRACTIONr_scbond_it2.49531393
X-RAY DIFFRACTIONr_scangle_it4.0484.51317
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1480TIGHT POSITIONAL0.040.05
1440LOOSE POSITIONAL0.055
1480TIGHT THERMAL0.130.5
1440LOOSE THERMAL0.1510
2356TIGHT POSITIONAL0.060.05
2373LOOSE POSITIONAL0.075
2356TIGHT THERMAL0.110.5
2373LOOSE THERMAL0.1310
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 85 -
Rwork0.252 1528 -
obs--95.44 %
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)
13.8757-0.3957-0.65252.4314-0.37992.8109-0.084-0.1199-0.27530.06040.07090.17270.32840.05940.01310.2443-0.013-0.00840.1279-0.00980.157135.82730.273-11.421
214.043-2.2286-2.35186.46240.63761.5237-0.01730.26-2.0722-0.1773-0.1441-0.33470.0717-0.05640.16130.1618-0.00970.00650.0797-0.00170.604129.17711.66-47.114
34.25010.3443-0.82152.41920.16483.3952-0.03420.2031-0.2333-0.040.0142-0.14960.2693-0.07270.020.20930.0221-0.0050.1449-0.02040.131862.35130.416-18.275
42.97620.382-0.68337.7618-1.02362.6595-0.0220.0933-0.0730.07520.180.67960.1328-0.1134-0.1580.0953-0.0005-0.00370.01060.00020.190969.89110.67216.072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 141
2X-RAY DIFFRACTION2A148 - 246
3X-RAY DIFFRACTION3B18 - 141
4X-RAY DIFFRACTION4B150 - 246

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