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- PDB-2vii: PspF1-275-Mg-AMP -

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Basic information

Entry
Database: PDB / ID: 2vii
TitlePspF1-275-Mg-AMP
ComponentsPSP OPERON TRANSCRIPTIONAL ACTIVATOR
KeywordsTRANSCRIPTION / AAA / PSPF / ACTIVATOR / ATP-BINDING / DNA-BINDING / SIGMA54 ACTIVATOR / NUCLEOTIDE-BINDING / GENE REGULATION / ENHANCER BINDING PROTEIN / TRANSCRIPTION ACTIVATION / TRANSCRIPTION REGULATION / TWO-COMPONENT REGULATORY SYSTEM
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
ADENOSINE MONOPHOSPHATE / Psp operon transcriptional activator
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsJoly, N. / Rappas, M. / Buck, M. / Zhang, X.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Trapping of a Transcription Complex Using a New Nucleotide Analogue: AMP Aluminium Fluoride
Authors: Joly, N. / Rappas, M. / Buck, M. / Zhang, X.
History
DepositionDec 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)29,7623
Polymers29,3911
Non-polymers3722
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.607, 113.607, 39.358
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


Mass: 29390.668 Da / Num. of mol.: 1 / Fragment: AAA DOMAIN, RESIDUES 1-259
Source method: isolated from a genetically manipulated source
Details: ADENOSINE MONOPHOSPHATE (AMP) / 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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES WITH MISSING SIDE CHAINS WERE MODELED 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: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8
Details: 0.1M TRIS-HCL PH 8.0, 2.0M AMMONIUM FORMATE, 10% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9757
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 23, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 2.85→98.39 Å / Num. obs: 6998 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.7
Reflection shellResolution: 2.85→3 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BJW

2bjw


Resolution: 2.85→98.39 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1239789.71 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 348 5 %RANDOM
Rwork0.186 ---
obs0.186 6985 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2532 Å2 / ksol: 0.364526 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å25.33 Å20 Å2
2---2.44 Å20 Å2
3---4.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.85→98.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 24 107 2086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 52 4.5 %
Rwork0.248 1096 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3AMP.PARAMP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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