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- PDB-4bg7: Bacteriophage T5 Homolog of the Eukaryotic Transcription Coactiva... -

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Basic information

Entry
Database: PDB / ID: 4bg7
TitleBacteriophage T5 Homolog of the Eukaryotic Transcription Coactivator PC4 Implicated in Recombination-Dependent DNA Replication
ComponentsPUTATIVE TRANSCRIPTIONAL COACTIVATOR P15
KeywordsREPLICATION / RECOMBINATION / REPAIR / TRANSCRIPTION / SSB
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
Transcriptional coactivator p15 (PC4) C-terminal domain-containing protein
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsSteigemann, B. / Schulz, A. / Hinrichs, W. / Werten, S.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Bacteriophage T5 Encodes a Homolog of the Eukaryotic Transcription Coactivator Pc4 Implicated in Recombination-Dependent DNA Replication.
Authors: Steigemann, B. / Schulz, A. / Werten, S.
History
DepositionMar 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE TRANSCRIPTIONAL COACTIVATOR P15
B: PUTATIVE TRANSCRIPTIONAL COACTIVATOR P15


Theoretical massNumber of molelcules
Total (without water)24,1092
Polymers24,1092
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-41.5 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.570, 108.570, 34.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein PUTATIVE TRANSCRIPTIONAL COACTIVATOR P15 / BACTERIOPHAGE T5 HOMOLOG OF PC4


Mass: 12054.358 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T5 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6QGH2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.12 Å3/Da / Density % sol: 41.9 % / Description: NONE
Crystal growpH: 6.5
Details: 100 MM SODIUM ACETATE PH 6.5, 20% PEG 4000, 8% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 16230 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 36.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.193 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25731 816 5 %RANDOM
Rwork0.19769 ---
obs0.20054 15406 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.255 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 0 93 1642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021587
X-RAY DIFFRACTIONr_bond_other_d0.0020.021068
X-RAY DIFFRACTIONr_angle_refined_deg1.791.9362150
X-RAY DIFFRACTIONr_angle_other_deg0.96632589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5124.77388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0615275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.74158
X-RAY DIFFRACTIONr_chiral_restr0.1180.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02350
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 66 -
Rwork0.285 1033 -
obs--99.28 %

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