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- PDB-4l9g: Structure of PpsR N-Q-PAS1 from Rb. sphaeroides -

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Basic information

Entry
Database: PDB / ID: 4l9g
TitleStructure of PpsR N-Q-PAS1 from Rb. sphaeroides
ComponentsTranscriptional regulator, PpsR
KeywordsTRANSCRIPTION / PAS domain / Per-Arnt-Sim / Oligomerization / AppA
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 / molecular replacement / Resolution: 2.2 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
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, PpsR
B: Transcriptional regulator, PpsR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2507
Polymers57,6702
Non-polymers5795
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-94 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.400, 107.910, 92.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transcriptional regulator, PpsR


Mass: 28835.143 Da / Num. of mol.: 2 / Fragment: UNP residues 2-257
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 0.1 M 2-(N-morpholino)ethanesulfonic acid, 0.01 M L-cysteine, 4% (v/v) 1,4-dioxane, 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: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2012 / Details: Dynamically bendable mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionNumber: 113562 / Rmerge(I) obs: 0.104 / D res high: 2.2 Å / Num. obs: 26156 / % possible obs: 99.8
ReflectionResolution: 2.2→50 Å / Num. all: 26156 / Num. obs: 26156 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 38.428 Å2 / Net I/σ(I): 10.37
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.2-2.30.6312.38134943183199.7
2.3-2.40.5132.95119202701199.9
2.4-2.50.4443.56104002279199.7
2.5-2.70.324.58159203629199.9
2.7-30.2066.89165493830199.9
3-40.08214.99261785974199.9
4-60.04624.42133533137199.6
6-100.04325.445361093199.6
10-500.02931.871212330198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.65 Å46.55 Å
Translation4.65 Å46.55 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.0phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PpsR Q-PAS1

Resolution: 2.2→46.549 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8426 / SU ML: 0.27 / σ(F): 0 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 1307 5 %random
Rwork0.1767 ---
obs0.1795 26150 99.78 %-
all-26150 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.78 Å2 / Biso mean: 44.1715 Å2 / Biso min: 19.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 32 147 4041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013945
X-RAY DIFFRACTIONf_angle_d1.2095340
X-RAY DIFFRACTIONf_chiral_restr0.075616
X-RAY DIFFRACTIONf_plane_restr0.005703
X-RAY DIFFRACTIONf_dihedral_angle_d14.3881523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.28810.31791420.237526962838100
2.2881-2.39220.27241420.210927112853100
2.3922-2.51840.25391430.199227142857100
2.5184-2.67610.26051450.197327402885100
2.6761-2.88270.25741420.195827162858100
2.8827-3.17280.25771460.183827612907100
3.1728-3.63170.22971460.174927722918100
3.6317-4.5750.1981480.142628112959100
4.575-46.5490.20581530.16632922307599
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)
14.85691.21890.26253.05420.09843.5310.0170.1620.1519-0.08770.01430.00590.05640.0231-0.03160.24820.0140.00310.29080.03260.2602-4.448515.712-22.2929
26.6836-3.80529.53880.7732-4.42118.75220.38030.87480.0141-0.354-0.4984-0.01650.89990.86180.03570.4382-0.0023-0.05260.63540.00330.430316.46613.370514.0081
33.52430.80790.16823.23790.54611.88190.0091-0.068-0.05650.0762-0.02570.1070.0414-0.15440.00960.20380.0087-0.01670.2792-0.00150.253816.530713.073945.5042
45.47890.21-1.453.67770.89927.1465-0.0384-0.34920.31530.23230.10440.50250.1506-0.2945-0.05410.2345-0.041-0.00990.34880.00620.4331-23.355316.5271-9.2187
56.35141.74695.95960.51411.41875.8344-0.4995-0.04130.2095-0.22130.16390.1065-0.3358-0.50380.3210.3509-0.0152-0.04420.56870.01090.489810.503316.747118.1198
65.21070.1157-0.36373.1067-0.2392.88540.01290.3338-0.209-0.27930.0547-0.20510.26620.0311-0.07740.22170.01110.00920.2567-0.00370.276342.611914.460130.3073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 8:120)A8 - 120
2X-RAY DIFFRACTION2chain 'A' and (resseq 121:157)A121 - 157
3X-RAY DIFFRACTION3chain 'A' and (resseq 158:257)A158 - 257
4X-RAY DIFFRACTION4chain 'B' and (resseq 6:120)B6 - 120
5X-RAY DIFFRACTION5chain 'B' and (resseq 121:157)B121 - 157
6X-RAY DIFFRACTION6chain 'B' and (resseq 158:257)B158 - 257

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