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- PDB-4blp: P4 PROTEIN FROM BACTERIOPHAGE PHI13 -

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Basic information

Entry
Database: PDB / ID: 4blp
TitleP4 PROTEIN FROM BACTERIOPHAGE PHI13
ComponentsPACKAGING ENZYME P4
KeywordsHYDROLASE / NTPASE / CYSTOVIRIDAE
Function / homology
Function and homology information


viral genome packaging
Similarity search - Function
Packaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPSEUDOMONAS PHAGE PHI13 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsEl Omari, K. / Meier, C. / Kainov, D. / Sutton, G. / Grimes, J.M. / Poranen, M.M. / Bamford, D.H. / Tuma, R. / Stuart, D.I. / Mancini, E.J.
CitationJournal: Nucleic Acids Res / Year: 2013
Title: Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.
Authors: Kamel El Omari / Christoph Meier / Denis Kainov / Geoff Sutton / Jonathan M Grimes / Minna M Poranen / Dennis H Bamford / Roman Tuma / David I Stuart / Erika J Mancini /
Abstract: Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, ...Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected the mechanism of RNA translocation for one such phage, 12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from 6, 8 and 13). High-resolution crystal structures of the set of P4s allow a structure-based phylogenetic analysis, which reveals that these proteins form a distinct subfamily of the RecA-type ATPases. Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains. Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in 8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in 12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the 12 enzyme.
History
DepositionMay 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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: PACKAGING ENZYME P4
B: PACKAGING ENZYME P4
C: PACKAGING ENZYME P4
D: PACKAGING ENZYME P4
E: PACKAGING ENZYME P4
F: PACKAGING ENZYME P4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,08912
Polymers226,3426
Non-polymers7476
Water29,3101627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20380 Å2
ΔGint-106 kcal/mol
Surface area56260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.219, 116.239, 149.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PACKAGING ENZYME P4


Mass: 37723.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI13 (bacteriophage)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9FZT1
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1627 / 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7
Details: 100 MM TRIS-HCL PH 7.0, 900 MM TRISODIUM CITRATE AND 200MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 183932 / % possible obs: 99.3 % / Observed criterion σ(I): 2.4 / Redundancy: 4.3 % / Biso Wilson estimate: 16.96 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→19.85 Å / Cor.coef. Fo:Fc: 0.9577 / Cor.coef. Fo:Fc free: 0.9473 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 8472 5 %RANDOM
Rwork0.163 ---
obs0.1642 169434 91.06 %-
Displacement parametersBiso mean: 21.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.1917 Å20 Å20 Å2
2--0.7183 Å20 Å2
3----0.5266 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11812 0 50 1627 13489
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01212283HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0716869HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5653SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes259HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1880HARMONIC5
X-RAY DIFFRACTIONt_it12283HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.06
X-RAY DIFFRACTIONt_other_torsion2.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1713SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16359SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2358 278 4.95 %
Rwork0.2027 5334 -
all0.2043 5612 -
obs--91.06 %
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)
11.52160.2405-0.25650.5942-0.05990.6610.02590.11610.3676-0.04110.01720.0525-0.0763-0.016-0.0431-0.06070.0080.003-0.12250.02870.053919.52577.065411.9005
21.3381-0.1628-0.40830.61010.06240.6665-0.0102-0.04660.157-0.03940.0085-0.0808-0.02770.06950.0017-0.0516-0.02830.0036-0.0707-0.0068-0.007646.567966.093414.5579
30.901-0.0039-0.21130.83740.23410.5893-0.0278-0.1024-0.11960.0342-0.0013-0.10720.0310.1030.0291-0.05730.01190.0037-0.02350.0274-0.033850.796738.299922.3332
40.66930.035-0.03060.44980.04130.42890.0017-0.004-0.1215-0.0565-0.02960.01130.02560.03830.0279-0.03080.01520.0087-0.03030.0328-0.028327.482220.811226.9185
50.6677-0.05670.15810.6165-0.08410.5489-0.024-0.0278-0.0671-0.04640.04930.12020.0637-0.0212-0.0253-0.0389-0.01860.0033-0.03580.0328-0.01360.199931.177724.214
60.71640.16590.02280.6338-0.32220.7752-0.03590.05230.1202-0.03580.07050.09530.0233-0.1184-0.0346-0.05530.0066-0.0002-0.04630.0162-0.0189-3.616359.205115.5233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

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