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- PDB-2c99: Structural basis of the nucleotide driven conformational changes ... -

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Basic information

Entry
Database: PDB / ID: 2c99
TitleStructural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF
ComponentsPSP OPERON TRANSCRIPTIONAL ACTIVATOR
KeywordsTRANSCRIPTION REGULATION / BACTERIAL SIGMA54 ACTIVATOR / ATPASE / ATP-BINDING / DNA-BINDING / SENSORY TRANSDUCTION / TWO-COMPONENT REGULATORY SYSTEM
Function / homology
Function and homology information


regulation of cellular response to stress / DNA-binding transcription activator activity / phosphorelay signal transduction system / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription regulator complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription ...regulation of cellular response to stress / DNA-binding transcription activator activity / phosphorelay signal transduction system / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Psp operon transcriptional activator
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRappas, M. / Schumacher, J. / Niwa, H. / Buck, M. / Zhang, X.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis of the Nucleotide Driven Conformational Changes in the Aaa(+) Domain of Transcription Activator Pspf.
Authors: Rappas, M. / Schumacher, J. / Niwa, H. / Buck, M. / Zhang, X.
History
DepositionDec 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 27, 2013Group: Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)30,4932
Polymers29,9871
Non-polymers5061
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.250, 113.250, 39.332
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: 29987.295 Da / Num. of mol.: 1 / Fragment: AAA DOMAIN, RESIDUES 1-265
Source method: isolated from a genetically manipulated source
Details: AMPPNP / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P37344
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRANSCRIPTIONAL ACTIVATOR FOR THE PHAGE SHOCK PROTEIN (PSP) OPERON (PSPABCE)
Sequence detailsDISORDERED RESIDUES HAVE BEEN MODELLED AS ALANINES

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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: 47 %
Crystal growpH: 8 / Details: 2M AMMONIUM FORMATE, 0.1 M HEPES PH 8.0, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 27, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 22409 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.9 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BJW

2bjw


Resolution: 1.9→100 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.838 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGION HAVE NOT BEEN MODELLED AND DISORDERED RESIDUES HAVE BEEN MODELLED AS ALANINES
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1101 4.9 %RANDOM
Rwork0.164 ---
obs0.166 21291 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0.37 Å20 Å2
2---0.75 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 31 200 2151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211991
X-RAY DIFFRACTIONr_bond_other_d0.0020.021844
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9972705
X-RAY DIFFRACTIONr_angle_other_deg1.04934268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0115241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3030.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022197
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02405
X-RAY DIFFRACTIONr_nbd_refined0.210.2407
X-RAY DIFFRACTIONr_nbd_other0.2520.22096
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3560.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3471.51212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45821945
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7323779
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1494.5760
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 68
Rwork0.188 1406
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)
10.6324-0.1929-0.09010.52130.16930.28310.05840.0539-0.0081-0.0366-0.062-0.0072-0.0145-0.02310.00360.03580.00920.00840.02060.0190.017523.0371-19.5859-5.0367
20.88960.01350.06910.2544-0.14060.3776-0.0095-0.03580.0214-0.0099-0.0137-0.00650.0039-0.00880.02320.021-0.0009-0.00280.0407-0.00440.022846.79861.99411.054
30000000000000000.0351000.035100.0351000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 178
2X-RAY DIFFRACTION2A179 - 257
3X-RAY DIFFRACTION3A303

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