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- PDB-4qos: CRYSTAL STRUCTURE OF PSPF(1-265) E108Q MUTANT bound to ADP -

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Basic information

Entry
Database: PDB / ID: 4qos
TitleCRYSTAL STRUCTURE OF PSPF(1-265) E108Q MUTANT bound to ADP
ComponentsPsp operon transcriptional activator
KeywordsTRANSCRIPTION / BACTERIAL SIGMA54 ACTIVATOR / ATPASE / ATP-BINDING / DNA-BINDING / SENSORY TRANSDUCTION / TRANSCRIPTION REGULATION / TWO-COMPONENT REGULATORY SYSTEM / AAA domain / Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene
Function / homology
Function and homology information


regulation of cellular response to stress / phosphorelay signal transduction system / transcription regulator complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding ...regulation of cellular response to stress / phosphorelay signal transduction system / transcription regulator complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Transcription activator PspF / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family ...Transcription activator PspF / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Psp operon transcriptional activator
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsDarbari, V.C. / Lawton, E. / Lu, D. / Burrows, P.C. / Wiesler, S. / Joly, N. / Zhang, N. / Zhang, X. / Buck, M.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Molecular basis of nucleotide-dependent substrate engagement and remodeling by an AAA+ activator.
Authors: Darbari, V.C. / Lawton, E. / Lu, D. / Burrows, P.C. / Wiesler, S. / Joly, N. / Zhang, N. / Zhang, X. / Buck, M.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Psp operon transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7444
Polymers29,9861
Non-polymers7583
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.385, 113.385, 39.326
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Psp operon transcriptional activator / Phage shock protein F


Mass: 29986.307 Da / Num. of mol.: 1 / Fragment: Phage Shock protein F AAA DOMAIN, RESIDUES 1-265 / Mutation: E108Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1303, JW1296, pspF, ycjB / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P37344
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Bis-Tris pH 8.0, 12-16% MPD, 2M Ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2013
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.42→28.35 Å / Num. all: 54883 / Num. obs: 54854 / % possible obs: 99.96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 18.58 Å2 / Rmerge(I) obs: 0.03967 / Rsym value: 0.04189 / Net I/σ(I): 28.76
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueDiffraction-ID% possible all
1.42-1.469.340310.619199.5
1.46-1.510.139020.4521100
1.5-1.5410.238230.3421100
1.54-1.5910.137300.2651100
1.59-1.649.936130.2181100
1.64-1.79.534660.171100
1.7-1.761033600.1371100
1.76-1.8310.332320.1091100
1.83-1.9110.231020.0841100
1.91-2.011029770.0661100
2.01-2.129.328360.0521100
2.12-2.249.726840.0441100
2.24-2.410.125540.0391100
2.4-2.599.923460.0351100
2.59-2.849.521800.0331100
2.84-3.178.919610.031100
3.17-3.679.817520.0281100
3.67-4.499.814920.0261100
4.49-6.358.911700.0251100
6.35-28.359.76640.026199

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1702)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJW

2bjw


Resolution: 1.42→28.35 Å / SU ML: 0.12349841607 / σ(F): 1.39 / Phase error: 18.1902345779 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2752 5.01713702326 %RANDOM
Rwork0.17 ---
all0.17 54883 --
obs0.17 54852 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.655 Å2
Refinement stepCycle: LAST / Resolution: 1.42→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 48 250 2193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009242908365312012
X-RAY DIFFRACTIONf_angle_d1.340138591912736
X-RAY DIFFRACTIONf_chiral_restr0.0706737790561303
X-RAY DIFFRACTIONf_plane_restr0.0063676410381354
X-RAY DIFFRACTIONf_dihedral_angle_d16.3797701685763
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4195-1.4440.262267401451350.2430639443342544254499.2589848092
1.444-1.47030.2543531950321440.22742493818626052605100
1.4703-1.49850.2066460351881250.21344541614326192619100
1.4985-1.52910.2408300855051240.20750547929125492549100
1.5291-1.56240.2357703817191280.2048613965092598259899.9633296663
1.5624-1.59870.2209158467081420.20037247458826222622100
1.5987-1.63870.2319961890791400.19950364920825922592100
1.6387-1.6830.2295873724671440.19127206813625552555100
1.683-1.73250.2270063968021390.19492421775825902590100
1.7325-1.78840.2288475867411510.18781614708225912591100
1.7884-1.85230.2098190408971400.18337327437325812581100
1.8523-1.92650.1964484824351290.18097675470126062606100
1.9265-2.01410.1919635366681300.16966336199326172617100
2.0141-2.12030.2020680328931410.16329578401525852585100
2.1203-2.25310.1799300042391540.15646733084225982598100
2.2531-2.42690.171360793691500.14949656150426002600100
2.4269-2.6710.1784132781651290.15329865574326362636100
2.671-3.05710.1520079180171520.15302355858826162616100
3.0571-3.85010.1843973255851200.15145323149726722672100
3.8501-28.35190.1772860118591350.1692591394252724272599.965034965

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