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- PDB-4qnm: CRYSTAL STRUCTURE of PSPF(1-265) E108Q MUTANT -

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Basic information

Entry
Database: PDB / ID: 4qnm
TitleCRYSTAL STRUCTURE of PSPF(1-265) E108Q MUTANT
ComponentsPsp operon transcriptional activator
KeywordsTRANSCRIPTION / AAA domain / Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene / ATP Binding / DNA binding
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
Psp operon transcriptional activator
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.628 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 18, 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

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Assembly

Deposited unit
A: Psp operon transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3173
Polymers29,9861
Non-polymers3302
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.721, 113.721, 39.453
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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-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
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
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: I04 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2013 / Details: Mirrors
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.628→28.43 Å / Num. all: 36835 / Num. obs: 36572 / % possible obs: 99.35 % / Observed criterion σ(F): 6.68 / Observed criterion σ(I): 5.76 / Redundancy: 8.3 % / Biso Wilson estimate: 23.35 Å2 / Rmerge(I) obs: 0.05594 / Rsym value: 0.05969 / Net I/σ(I): 21.1
Reflection shellResolution: 1.628→1.686 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.8913 / Mean I/σ(I) obs: 2.08 / Num. unique all: 3380 / Rsym value: 0.62

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.04 Å28.39 Å
Translation6.04 Å28.39 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.5.2phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
GDAdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJW

2bjw


Resolution: 1.628→28.43 Å / FOM work R set: 0.861 / SU ML: 0.19 / σ(F): 1.37 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1826 4.99 %RANDOM
Rwork0.1718 ---
all0.1735 36835 --
obs0.1735 36572 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.72 Å2 / Biso mean: 30.99 Å2 / Biso min: 13.15 Å2
Refinement stepCycle: LAST / Resolution: 1.628→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1877 0 21 174 2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081963
X-RAY DIFFRACTIONf_angle_d1.1722669
X-RAY DIFFRACTIONf_chiral_restr0.05301
X-RAY DIFFRACTIONf_plane_restr0.006347
X-RAY DIFFRACTIONf_dihedral_angle_d13.531750
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.6283-1.67230.30821170.261524522569256991
1.6723-1.72150.25851340.2384267528092809100
1.7215-1.77710.27031400.2118266728072807100
1.7771-1.84060.24391350.204264027752775100
1.8406-1.91420.2341300.1924271328432843100
1.9142-2.00130.21021310.1821268028112811100
2.0013-2.10680.21611530.1783266328162816100
2.1068-2.23880.19941530.1715265728102810100
2.2388-2.41150.21781540.169269128452845100
2.4115-2.65410.20521640.1724268028442844100
2.6541-3.03770.19171540.1692268328372837100
3.0377-3.82580.19681330.1552272328562856100
3.8258-28.43460.17881280.1618282229502950100

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