[English] 日本語
Yorodumi
- PDB-4bwy: P4 PROTEIN FROM BACTERIOPHAGE PHI8 (R32) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bwy
TitleP4 PROTEIN FROM BACTERIOPHAGE PHI8 (R32)
ComponentsP4
KeywordsHYDROLASE / NTPASE / CYSTOVIRIDAE
Function / homologyPackaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / viral genome packaging / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / p4
Function and homology information
Biological speciesPSEUDOMONAS PHAGE PHI8 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
DepositionJul 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P4
B: P4
C: P4
D: P4
E: P4
F: P4
G: P4
H: P4
I: P4
J: P4
K: P4
L: P4


Theoretical massNumber of molelcules
Total (without water)410,68712
Polymers410,68712
Non-polymers00
Water00
1
G: P4
H: P4
I: P4
J: P4
K: P4
L: P4


Theoretical massNumber of molelcules
Total (without water)205,3446
Polymers205,3446
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18980 Å2
ΔGint-90.1 kcal/mol
Surface area63130 Å2
MethodPISA
2
A: P4
B: P4
C: P4
D: P4
E: P4
F: P4


Theoretical massNumber of molelcules
Total (without water)205,3446
Polymers205,3446
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17480 Å2
ΔGint-79.7 kcal/mol
Surface area63190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.725, 197.725, 562.576
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein
P4 / PHI8 P4


Mass: 34223.945 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI8 (bacteriophage) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9MC14

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 4.6
Details: 100 MM SODIUM ACETATE PH 4.6 AND 2.2 M AMMONIUM SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.1→45 Å / Num. obs: 76933 / % possible obs: 100 % / Observed criterion σ(I): 1.3 / Redundancy: 12.7 % / Biso Wilson estimate: 67.67 Å2 / Rmerge(I) obs: 0.31 / Net I/σ(I): 8.6
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.3 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BLQ

4blq


Resolution: 3.1→45.39 Å / Cor.coef. Fo:Fc: 0.8189 / Cor.coef. Fo:Fc free: 0.7971 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.533
RfactorNum. reflection% reflectionSelection details
Rfree0.3086 3862 5.02 %RANDOM
Rwork0.2955 ---
obs0.2961 76933 99.89 %-
Displacement parametersBiso mean: 67.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.6601 Å20 Å20 Å2
2---1.6601 Å20 Å2
3---3.3202 Å2
Refine analyzeLuzzati coordinate error obs: 0.908 Å
Refinement stepCycle: LAST / Resolution: 3.1→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25719 0 0 0 25719
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00826016HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0835170HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12272SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes606HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3863HARMONIC5
X-RAY DIFFRACTIONt_it26016HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion2.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3494SEMIHARMONIC5
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_contact28802SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3047 283 5.03 %
Rwork0.2964 5346 -
all0.2968 5629 -
obs--99.89 %
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)
11.22370.21170.1110.53670.00362.2778-0.01850.02630.15940.007-0.00080.1521-0.00590.03480.0193-0.04140.0231-0.0038-0.07670.00910.141617.176894.7964-8.4408
22.31080.02621.51341.3041-1.00151.1508-0.02230.136-0.1075-0.0914-0.0099-0.1353-0.00070.05570.03220.049-0.01580.03040.0663-0.0925-0.080648.977161.6739-37.3785
32.2879-0.01861.36091.6654-0.13151.4741-0.01750.07090.08470.0074-0.0166-0.1136-0.05810.0430.03410.0099-0.04580.0224-0.0450.0638-0.009143.376589.9689-24.9108
43.3445-1.22070.18771.5305-1.25142.5038-0.0150.0259-0.1245-0.08610.01140.01860.1175-0.00650.00360.0666-0.0689-0.1207-0.1654-0.14710.039228.12838.3357-33.4929
51.0516-0.78020.61013.6177-0.86971.9673-0.0634-0.0671-0.06510.1116-0.00190.12190.1679-0.11540.06530.0062-0.1076-0.076-0.0382-0.01490.04471.311842.4401-14.8071
61.43160.5730.36241.0695-0.7672.1851-0.0034-0.04110.02220.04720.0140.15770.0124-0.0888-0.0106-0.0727-0.0192-0.0243-0.03270.02790.1073-3.615871.5105-4.2917
71.25630.3675-0.30120.8105-0.16972.67560.00580.0158-0.2331-0.0161-0.01210.00140.0015-0.01130.0063-0.06760.0393-0.0275-0.1197-0.00250.1662-8.223824.4946-85.6024
81.36930.35270.21711.4114-1.24121.26930.0172-0.10320.05340.0335-0.02250.0291-0.0641-0.00980.0053-0.0199-0.02610.07370.1091-0.0927-0.0563-20.940468.2482-56.3149
92.47980.019-0.36732.0254-1.02081.49390.0252-0.08420.00580.0617-0.0175-0.05850.0080.1149-0.0077-0.08160.0433-0.02040.0612-0.0302-0.04860.715449.3755-68.9002
100.95170.37660.93123.7984-1.67592.0758-0.0302-0.04130.05790.05730.00610.1607-0.0753-0.08070.024-0.17070.09260.14190.0602-0.06440.0713-51.658961.9684-60.3101
111.3575-1.03450.062.1623-0.71111.6880.03820.0423-0.109-0.1324-0.07460.1773-0.0245-0.18740.0364-0.2432-0.02810.07110.1134-0.0160.1704-60.542436.8676-77.0083
122.04410.52810.82270.7175-1.13343.19650.0454-0.0362-0.1576-0.0307-0.03520.05460.0636-0.0962-0.0102-0.0826-0.04750.0222-0.097-0.02570.1153-38.746218.1088-89.7304
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more