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- PDB-4l9f: Structure of a SeMet derivative of PpsR Q-PAS1 from Rb. sphaeroides -

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Basic information

Entry
Database: PDB / ID: 4l9f
TitleStructure of a SeMet derivative of PpsR Q-PAS1 from Rb. sphaeroides
ComponentsTranscriptional regulator, PpsRTranscriptional regulation
KeywordsTRANSCRIPTION / PAS domain / Per-Arnt-Sim / oligomerization
Function / homology
Function and homology information


sequence-specific DNA binding / identical protein binding
Similarity search - Function
Transcription regulator PpsR / 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 ...Transcription regulator PpsR / 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 / PAS domain superfamily / Homeobox-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, PpsR
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsHeintz, U. / Meinhart, A. / Schlichting, I. / Winkler, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides.
Authors: Heintz, U. / Meinhart, A. / Winkler, A.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, PpsR


Theoretical massNumber of molelcules
Total (without water)15,6481
Polymers15,6481
Non-polymers00
Water39622
1
A: Transcriptional regulator, PpsR

A: Transcriptional regulator, PpsR


Theoretical massNumber of molelcules
Total (without water)31,2962
Polymers31,2962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Buried area2590 Å2
ΔGint-20 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.610, 50.610, 163.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

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Components

#1: Protein Transcriptional regulator, PpsR / Transcriptional regulation


Mass: 15647.906 Da / Num. of mol.: 1 / Fragment: UNP residues 123-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.93 Å3/Da / Density % sol: 36.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3% (w/v) PEG 4000, 0.2 M magnesium chloride, 0.1 M 2-(N-morpholino)ethanesulfonic acid, 5 mM dithioerythritol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 4, 2012 / Details: Dynamically bendable mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionNumber: 331072 / Rmerge(I) obs: 0.148 / D res high: 2.5 Å / Num. obs: 8108 / % possible obs: 100
ReflectionResolution: 2.5→50 Å / Num. obs: 4783 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 40.8 % / Biso Wilson estimate: 39.379 Å2 / Net I/σ(I): 26.87
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.5-2.60.776.4334236887199.8
2.6-2.70.657.9301387671100
2.7-2.80.5219.78269276821100
2.8-30.40812.7453921071199.8
3-40.16426.8111309527121100
4-60.07353.265714213941100
6-100.06259.84191454671100
10-500.03885.4149971281100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHENIX-AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→42.3 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 0 / Phase error: 20.8 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 240 5.02 %RANDOM
Rwork0.193 ---
obs0.1954 4783 99.96 %-
all-4783 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.7 Å2 / Biso mean: 41.3306 Å2 / Biso min: 16.31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 0 22 883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009867
X-RAY DIFFRACTIONf_angle_d1.1921165
X-RAY DIFFRACTIONf_chiral_restr0.07139
X-RAY DIFFRACTIONf_plane_restr0.005152
X-RAY DIFFRACTIONf_dihedral_angle_d14.131339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-3.150.25261160.184321892305
3.15-42.30.23141240.196423542478
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)
15.11181.46761.49217.1413.25134.17530.4157-0.4579-0.30110.4722-0.53491.65520.211-1.45210.10480.3478-0.01360.10720.49770.00430.5631-2.9877-1.843585.412
24.7183-0.2310.30634.0218-0.50493.17420.0690.33350.2314-0.13710.03180.1846-0.1937-0.1387-0.1020.23740.00690.02730.27540.00540.29868.673815.288582.7423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 143 through 157)A0
2X-RAY DIFFRACTION2chain 'A' and (resid 158 through 257 )A0

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