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- PDB-4blo: P4 PROTEIN FROM BACTERIOPHAGE PHI6 IN COMPLEX WITH ADP -

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Basic information

Entry
Database: PDB / ID: 4blo
TitleP4 PROTEIN FROM BACTERIOPHAGE PHI6 IN COMPLEX WITH ADP
ComponentsPACKAGING ENZYME P4
KeywordsHYDROLASE / ATPASE / CYSTOVIRIDAE
Function / homology
Function and homology information


viral procapsid / viral genome packaging / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / ATP binding
Similarity search - Function
Packaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Packaging enzyme P4
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHI6 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_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: PACKAGING ENZYME P4
B: PACKAGING ENZYME P4
C: PACKAGING ENZYME P4
D: PACKAGING ENZYME P4
E: PACKAGING ENZYME P4
F: PACKAGING ENZYME P4
G: PACKAGING ENZYME P4
H: PACKAGING ENZYME P4
I: PACKAGING ENZYME P4
J: PACKAGING ENZYME P4
K: PACKAGING ENZYME P4
L: PACKAGING ENZYME P4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,75236
Polymers392,14512
Non-polymers5,60724
Water00
1
A: PACKAGING ENZYME P4
B: PACKAGING ENZYME P4
I: PACKAGING ENZYME P4
J: PACKAGING ENZYME P4
K: PACKAGING ENZYME P4
L: PACKAGING ENZYME P4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,87618
Polymers196,0726
Non-polymers2,80412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26420 Å2
ΔGint-196.1 kcal/mol
Surface area52290 Å2
MethodPISA
2
C: PACKAGING ENZYME P4
D: PACKAGING ENZYME P4
E: PACKAGING ENZYME P4
F: PACKAGING ENZYME P4
G: PACKAGING ENZYME P4
H: PACKAGING ENZYME P4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,87618
Polymers196,0726
Non-polymers2,80412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26350 Å2
ΔGint-196 kcal/mol
Surface area52050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.840, 95.260, 98.330
Angle α, β, γ (deg.)82.46, 86.17, 64.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PACKAGING ENZYME P4


Mass: 32678.740 Da / Num. of mol.: 12 / Fragment: RESIDUES 1-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI6 (bacteriophage) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P11125, nucleoside-triphosphate phosphatase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 8 / Details: 6% PEG 4000 AND 90 MM SODIUM ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 72831 / % possible obs: 97 % / Observed criterion σ(I): 1.5 / Redundancy: 3 % / Biso Wilson estimate: 51.06 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.5 / % possible all: 88.2

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.99 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.378
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 3663 5.03 %RANDOM
Rwork0.217 ---
obs0.2183 72767 97.01 %-
Displacement parametersBiso mean: 56.95 Å2
Baniso -1Baniso -2Baniso -3
1-3.8007 Å2-4.9072 Å21.6679 Å2
2---5.431 Å2-0.795 Å2
3---1.6303 Å2
Refine analyzeLuzzati coordinate error obs: 0.477 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24101 0 336 0 24437
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00924810HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0533835HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11367SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes491HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3776HARMONIC5
X-RAY DIFFRACTIONt_it24810HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion2.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3463SEMIHARMONIC5
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_contact28045SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3226 224 4.71 %
Rwork0.2777 4532 -
all0.2797 4756 -
obs--97.01 %
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)
12.1586-0.27740.79541.49690.45782.5319-0.0936-0.24480.01250.0585-0.10740.0891-0.2181-0.35620.2011-0.13830.1741-0.03920.3176-0.2058-0.226314.371666.025874.8786
22.1068-0.5862-0.39260.87220.86132.6761-0.1264-0.2918-0.03510.02750.10460.0228-0.02770.35670.0218-0.17790.0959-0.03130.4106-0.0863-0.214342.419552.663274.6887
33.3481-0.6107-0.01541.38680.08422.9130.1472-0.3156-0.48810.26570.0719-0.04180.24810.0382-0.2191-0.01330.2651-0.2570.142-0.1149-0.123417.33741.023225.8429
42.225-0.69790.37762.65890.95153.6473-0.01050.1423-0.33620.21290.4049-0.40830.48850.372-0.3945-0.19150.3899-0.15680.217-0.3478-0.043231.4586-7.4904-0.5237
52.5591-0.55360.43971.38540.83852.75150.1210.3579-0.3045-0.24460.2129-0.05280.20090.0842-0.3339-0.11320.1817-0.05790.3054-0.3445-0.187517.1671-3.5393-27.8774
62.0308-0.3093-0.36721.81140.61632.2108-0.00260.0673-0.0898-0.1319-0.0380.12620.084-0.08320.0406-0.05690.2107-0.16270.2597-0.2467-0.1642-11.32979.3786-28.9638
71.9815-0.14170.1070.9857-0.26882.81940.03860.0688-0.18880.0234-0.05060.09310.235-0.09490.0119-0.14870.1938-0.1160.2624-0.2381-0.1087-25.529417.7268-2.4715
83.5502-1.190.08581.75730.27771.6779-0.0829-0.4539-0.16750.0940.07130.15290.1334-0.27910.0116-0.15430.1325-0.05160.3651-0.1308-0.2238-11.128213.382724.9203
92.0969-0.3580.12671.2890.59692.0402-0.1661-0.1037-0.14030.13750.12820.08050.16940.20140.0379-0.16630.1230.03920.3682-0.1119-0.180153.699540.412348.3066
102.7464-1.06750.73541.5311-0.33042.35490.14810.2001-0.1487-0.028-0.07280.02330.08810.1171-0.0754-0.16750.0756-0.01120.3301-0.2175-0.20937.171241.548722.0726
112.0477-0.6692-0.09611.09410.35872.55050.05880.2904-0.3318-0.0453-0.15060.1863-0.2264-0.10220.0917-0.16670.1313-0.06570.3409-0.2318-0.20578.889854.901722.3588
122.04640.30420.75270.92290.44893.2585-0.2607-0.15340.106-0.0743-0.06810.0367-0.4948-0.490.3288-0.15220.299-0.11090.3265-0.2261-0.1926-2.647767.08248.7524
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
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L

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