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- PDB-4hh2: Structure of PpsR without the HTH motif from Rb. sphaeroides -

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Basic information

Entry
Database: PDB / ID: 4hh2
TitleStructure of PpsR without the HTH motif from Rb. sphaeroides
ComponentsTranscriptional regulator, PpsR
KeywordsTRANSCRIPTION / triple PAS domain / Q-linker / DNA-binding / AppA
Function / homology
Function and homology information


sequence-specific DNA binding / identical protein binding
Similarity search - Function
Transcription regulator PpsR / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / PAS domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / PAS domain / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. ...Transcription regulator PpsR / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / PAS domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / PAS domain / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PAS domain superfamily / Homeobox-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, PpsR
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsWinkler, A. / Heintz, U. / Lindner, R. / Reinstein, J. / Shoeman, R. / Schlichting, I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression.
Authors: Winkler, A. / Heintz, U. / Lindner, R. / Reinstein, J. / Shoeman, R.L. / Schlichting, I.
History
DepositionOct 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, PpsR
B: Transcriptional regulator, PpsR
C: Transcriptional regulator, PpsR
D: Transcriptional regulator, PpsR


Theoretical massNumber of molelcules
Total (without water)168,6164
Polymers168,6164
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26870 Å2
ΔGint-127 kcal/mol
Surface area64440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.450, 117.450, 211.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Transcriptional regulator, PpsR


Mass: 42153.984 Da / Num. of mol.: 4 / Fragment: UNP residues 2-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: ppsR, RHOS4_18870, RSP_0282 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q3J179
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 50.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M tris chloride buffer, 1.9M ammonium sulfate, 12% glycerol, 6% xylitol, 1% dioxane, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9483 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011 / Details: Dynamically bendable mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9483 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 42372 / Num. obs: 41955 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 110.1 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 17.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX-AutoSolmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX-AutoSolphasing
RefinementResolution: 2.8→46.971 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 2010 4.79 %
Rwork0.1815 --
obs0.1841 41952 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→46.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11484 0 0 11 11495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511638
X-RAY DIFFRACTIONf_angle_d0.84215759
X-RAY DIFFRACTIONf_dihedral_angle_d13.624417
X-RAY DIFFRACTIONf_chiral_restr0.0581842
X-RAY DIFFRACTIONf_plane_restr0.0032089
LS refinement shellResolution: 2.8001→2.8701 Å
RfactorNum. reflection% reflection
Rfree0.36 141 -
Rwork0.2893 2824 -
obs--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)
15.0659-3.74360.19996.11371.32250.0179-0.24281.38620.5332-0.4751-0.1841-0.1888-0.048-0.08190.36480.5487-0.2254-0.11010.89890.02850.694337.146565.693340.4053
22.59343.9619-1.03798.57440.11156.19060.0052-0.54071.31640.60790.0071.0827-0.3346-0.674-0.09120.5447-0.0480.21250.735-0.17531.218669.3282100.313696.7183
33.9013.46888.08150.27973.04545.7614-0.22250.13040.6811-0.2756-0.49930.62970.4361-0.8250.2260.6705-0.0243-0.09030.98140.01220.803160.663278.060673.2205
41.4497-0.93361.78093.2734-3.59213.1455-0.4361-0.90370.62870.67670.031-0.5475-0.69640.21440.18570.87010.0725-0.37940.6262-0.18170.70881.485270.0583127.1949
55.95480.1042-1.42142.87824.10516.57840.16080.39850.54660.2206-0.18680.5653-0.525-0.8381-0.02560.70060.0063-0.17740.85520.01711.150827.745386.004644.4151
63.53352.09116.1302-0.3212.22852.7693-0.0285-0.02931.12530.1053-0.71220.5390.8504-0.63660.86230.7871-0.1271-0.07090.994-0.03990.847360.092185.429371.9818
76.91460.90540.02137.4206-2.6645.5595-0.1839-0.0708-0.4180.0211-0.0884-1.01730.12430.81210.17740.3763-0.09090.02990.4892-0.00640.546883.154773.335292.5171
84.00091.26950.86262.6636-0.5842.8543-0.2823-0.77360.08420.37120.07190.398-0.23-0.77870.18210.56270.2134-0.04530.7324-0.07020.545264.85967.4779116.8155
98.2844-1.2212-0.22023.29693.04856.1612-0.6142-0.66910.93760.74750.5225-0.299-0.0728-0.65780.27941.14430.0747-0.36360.6579-0.02590.748992.753358.9889155.7329
104.21294.91616.42766.1296.16238.102-0.1724-0.66330.16540.3858-0.79860.74950.2191-1.27540.65120.7066-0.016-0.04020.9155-0.00070.556878.083141.8146119.0963
111.2479-2.7924-4.05925.04964.56935.5384-0.5616-0.28420.8195-0.08560.5647-1.3359-0.42341.9198-0.21011.0272-0.4039-0.29781.18170.01521.0789111.326661.5744142.2283
128.43842.01310.1936-0.33240.88937.11330.134-0.29080.4970.1351-0.7183-0.13270.50350.02760.39510.78660.0985-0.24520.8089-0.04470.856980.726949.3589116.4758
135.5632.28442.87926.729-2.63266.98440.29140.3817-0.33120.1538-0.41010.38330.6043-0.59170.04370.7472-0.23890.10570.7302-0.23150.759154.337532.189104.8016
142.8791-0.74521.81936.4342-3.65270.78130.0480.47620.0297-0.47270.04030.277-0.2939-0.15030.05570.5357-0.093-0.04310.6813-0.1340.305543.139162.734773.8255
157.0640.7775-0.96878.1620.94586.1542-0.09180.7245-0.2657-0.7391-0.0635-0.87410.10250.10330.12860.5081-0.05250.07290.4886-0.09920.422372.155649.256587.708
162.2844-2.47331.20623.62632.37685.1006-0.1336-0.35720.28680.2925-0.0738-0.0708-0.0973-0.39520.06930.4879-0.04150.02380.471-0.0030.41648.317669.271791.5182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 120 )A6 - 120
2X-RAY DIFFRACTION2chain 'A' and (resid 158 through 255 )A158 - 255
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 157 )A121 - 157
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 378 )A256 - 378
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 120 )B6 - 120
6X-RAY DIFFRACTION6chain 'B' and (resid 121 through 157 )B121 - 157
7X-RAY DIFFRACTION7chain 'B' and (resid 158 through 255 )B158 - 255
8X-RAY DIFFRACTION8chain 'B' and (resid 256 through 378 )B256 - 378
9X-RAY DIFFRACTION9chain 'C' and (resid 6 through 120 )C6 - 120
10X-RAY DIFFRACTION10chain 'C' and (resid 121 through 157 )C121 - 157
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 120 )D6 - 120
12X-RAY DIFFRACTION12chain 'D' and (resid 121 through 157 )D121 - 157
13X-RAY DIFFRACTION13chain 'D' and (resid 158 through 255 )D158 - 255
14X-RAY DIFFRACTION14chain 'D' and (resid 256 through 378 )D256 - 378
15X-RAY DIFFRACTION15chain 'C' and (resid 158 through 255 )C158 - 255
16X-RAY DIFFRACTION16chain 'C' and (resid 256 through 378 )C256 - 378

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