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- PDB-4dvd: Crystal structure of the disulphide linked knotted homodimer of Psu -

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Basic information

Entry
Database: PDB / ID: 4dvd
TitleCrystal structure of the disulphide linked knotted homodimer of Psu
ComponentsPolarity suppression protein
KeywordsTRANSCRIPTION REGULATOR / All alpha protein / transcription termination inhibitor / Rho binding / capsid decoration protein of bacteriophage P4 / Transcription terminator Rho helicase
Function / homologyPhage polarity suppression protein monomer / symbiont-mediated activation of host transcription / Bacteriophage P4, Psu, polarity suppression protein / Phage polarity suppression protein (Psu) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / Polarity suppression protein
Function and homology information
Biological speciesEnterobacteria phage P4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBanerjee, R. / Nath, S. / Sen, U.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The first structure of polarity suppression protein, Psu from enterobacteria phage P4, reveals a novel fold and a knotted dimer
Authors: Banerjee, R. / Nath, S. / Ranjan, A. / Khamrui, S. / Pani, B. / Sen, R. / Sen, U.
History
DepositionFeb 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polarity suppression protein


Theoretical massNumber of molelcules
Total (without water)21,3631
Polymers21,3631
Non-polymers00
Water00
1
A: Polarity suppression protein

A: Polarity suppression protein


Theoretical massNumber of molelcules
Total (without water)42,7262
Polymers42,7262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area4700 Å2
ΔGint-51 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.610, 149.610, 62.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Polarity suppression protein / Amber mutation-suppressing protein


Mass: 21362.973 Da / Num. of mol.: 1 / Mutation: C13S,C117S,T123C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P4 (virus) / Gene: psu / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P05460
Has protein modificationY

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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: 4.11 Å3/Da / Density % sol: 70.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7.5%(w/v) PEG 6000, 5%(v/v) glycerol, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 15, 2012 / Details: Osmic maxflux
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→47.311 Å / Num. obs: 6846 / % possible obs: 94.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 51.09 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.16 Å / % possible all: 93.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RX6

3rx6


Resolution: 3→47.311 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.7767 / SU ML: 0.61 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 320 4.68 %RANDOM
Rwork0.231 ---
obs0.233 6838 92.29 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.695 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 136.92 Å2 / Biso mean: 58.1161 Å2 / Biso min: 21.27 Å2
Baniso -1Baniso -2Baniso -3
1-7.9983 Å20 Å20 Å2
2--7.9983 Å20 Å2
3----15.9965 Å2
Refinement stepCycle: LAST / Resolution: 3→47.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 0 0 1477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111501
X-RAY DIFFRACTIONf_angle_d1.2522027
X-RAY DIFFRACTIONf_chiral_restr0.068225
X-RAY DIFFRACTIONf_plane_restr0.005270
X-RAY DIFFRACTIONf_dihedral_angle_d16.118567
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0003-3.77990.32411530.26283214336793
3.7799-47.31670.24581670.21293304347192

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