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- PDB-2bjv: Crystal Structure of PspF(1-275) R168A mutant -

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Basic information

Entry
Database: PDB / ID: 2bjv
TitleCrystal Structure of PspF(1-275) R168A mutant
ComponentsPSP OPERON TRANSCRIPTIONAL ACTIVATOR
KeywordsTRANSCRIPTION / AAA / TRANSCRIPTION ACTIVATION / GENE REGULATION / SIGMA54 ACTIVATOR / ENHANCER BINDING PROTEIN / PSPF / ATP-BINDING / DNA- BINDING / TRANSCRIPTION REGULATION
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 / MAD / Resolution: 1.7 Å
AuthorsRappas, M. / Schumacher, J. / Beuron, F. / Niwa, H. / Bordes, P. / Wigneshweraraj, S. / Keetch, C.A. / Robinson, C.V. / Buck, M. / Zhang, X.
CitationJournal: Science / Year: 2005
Title: Structural insights into the activity of enhancer-binding proteins.
Authors: Mathieu Rappas / Jorg Schumacher / Fabienne Beuron / Hajime Niwa / Patricia Bordes / Sivaramesh Wigneshweraraj / Catherine A Keetch / Carol V Robinson / Martin Buck / Xiaodong Zhang /
Abstract: Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic ...Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic electron microscopy (cryo-EM) a 20 angstrom resolution structure of an activator, phage shock protein F [PspF(1-275)], which is bound to an ATP transition state analog in complex with its basal factor, sigma54. By fitting the crystal structure of PspF(1-275) at 1.75 angstroms into the EM map, we identified two loops involved in binding sigma54. Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54.
History
DepositionFeb 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2017Group: Data collection / Category: diffrn_detector / reflns / reflns_shell
Item: _diffrn_detector.type / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PSP OPERON TRANSCRIPTIONAL ACTIVATOR


Theoretical massNumber of molelcules
Total (without water)29,9011
Polymers29,9011
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.613, 113.613, 39.145
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PSP OPERON TRANSCRIPTIONAL ACTIVATOR / PSPF / PHAGE SHOCK PROTEIN F


Mass: 29901.178 Da / Num. of mol.: 1 / Fragment: AAA DOMAIN, RESIDUES 1-265 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET28B PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P37344
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE CHAIN A, ARG 168 ALA

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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: 2.33 Å3/Da / Density % sol: 43 %
Crystal growpH: 8 / Details: 2 M AMMONIUM FORMATE, 0.1 MM HEPES PH 8.0, 10% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97, 1.1
DetectorType: ADSC / Detector: CCD / Date: Sep 28, 2003 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.11
ReflectionResolution: 1.7→37 Å / Num. obs: 29411 / % possible obs: 91.6 % / Observed criterion σ(I): 2.5 / Redundancy: 3.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 26
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3 / % possible all: 60.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→37 Å / Data cutoff high absF: 100000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELLED AS ALANINES
RfactorNum. reflection% reflectionSelection details
Rfree0.21244 2004 6.9 %RANDOM
Rwork0.17235 ---
obs0.17235 26845 91.6 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK / Bsol: 300 Å2 / ksol: 0.8 e/Å3
Displacement parametersBiso mean: 22.879 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0.56 Å20 Å2
2---1.11 Å20 Å2
3---1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 0 162 1986
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d5.38
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2361.5
X-RAY DIFFRACTIONc_mcangle_it2.2292
X-RAY DIFFRACTIONc_scbond_it3.333
X-RAY DIFFRACTIONc_scangle_it5.864.5
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 73 5 %
Rwork0.203 1144 -
obs--60.5 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAMS / Topol file: PROTEIN.TOP

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