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- PDB-4l9e: Structure of PpsR Q-PAS1 from Rb. sphaeroides -

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Basic information

Entry
Database: PDB / ID: 4l9e
TitleStructure 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 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
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Transcriptional regulator, PpsR


Theoretical massNumber of molelcules
Total (without water)15,3201
Polymers15,3201
Non-polymers00
Water1,47782
1
A: Transcriptional regulator, PpsR

A: Transcriptional regulator, PpsR


Theoretical massNumber of molelcules
Total (without water)30,6392
Polymers30,6392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2610 Å2
ΔGint-23 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.380, 50.380, 163.310
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-377-

HOH

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Components

#1: Protein Transcriptional regulator, PpsR / Transcriptional regulation


Mass: 15319.641 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.: 82 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.9% (w/v) PEG 3000, 0.2 M magnesium chloride, 0.1 M sodium cacodylate, 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: 0.9765 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: 0.9765 Å / Relative weight: 1
ReflectionNumber: 197155 / Rmerge(I) obs: 0.049 / D res high: 1.65 Å / Num. obs: 15633 / % possible obs: 99.9
ReflectionResolution: 1.65→50 Å / Num. all: 15633 / Num. obs: 15633 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 41.368 Å2 / Net I/σ(I): 21.06
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.65-1.70.5584.421649712991100
1.7-1.80.3796.142728522031100
1.8-1.90.2568.77223901735199.8
1.9-20.18612.23188951420199.7
2-2.50.10219.88544284235199.9
2.5-30.06530.88247801915199.9
3-40.04442.94186701566199.9
4-60.03852.5599148471100
6-100.03454.283388312199.7
10-500.02852.899081011100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4L9F
Resolution: 1.65→43.63 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.7682 / SU ML: 0.18 / σ(F): 0 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.219 798 5.11 %random
Rwork0.1967 ---
obs0.198 15633 99.9 %-
all-15633 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.59 Å2 / Biso mean: 42.392 Å2 / Biso min: 24.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 0 82 968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006903
X-RAY DIFFRACTIONf_angle_d0.9661220
X-RAY DIFFRACTIONf_chiral_restr0.068145
X-RAY DIFFRACTIONf_plane_restr0.006162
X-RAY DIFFRACTIONf_dihedral_angle_d10.749355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.75350.31571160.24924092525
1.7535-1.88890.28221330.231923862519
1.8889-2.07890.27871360.209324282564
2.0789-2.37970.23651410.197224282569
2.3797-2.99810.20191300.214424932623
2.9981-43.630.20581420.184526882830
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.30380.02072.94497.5098-1.08054.19560.31910.9452-0.5153-0.2383-0.3723-1.56530.43221.3486-0.11790.37990.08740.08260.41540.01340.48613.2705-1.5323-4.0289
24.6103-0.72960.75054.36340.2532.1459-0.0165-0.26120.20680.17270.0023-0.1066-0.165-0.05610.02150.2527-0.00130.02410.233-0.0150.2514-8.36215.0536-0.6997
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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