[English] 日本語
Yorodumi
- PDB-9f5m: Structure of the C-terminal domain of bacteriophage K gp155, native -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f5m
TitleStructure of the C-terminal domain of bacteriophage K gp155, native
ComponentsGP-PDE domain-containing protein
KeywordsVIRAL PROTEIN / glycerophosphoryl diester phosphodiesterase
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / GP-PDE domain-containing protein
Function and homology information
Biological speciesStaphylococcus phage K (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPichel, A. / van Raaij, M.J.
Funding support Spain, 3items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)BFU2014-53425-P Spain
Agencia Estatal de Investigacion (AEI)BFU2017-82207-P Spain
Agencia Estatal de Investigacion (AEI)PID2021-125597NB-I00 Spain
CitationJournal: to be published
Title: Structure of bacteriophage K gp155
Authors: Pichel, A. / van Raaij, M.J.
History
DepositionApr 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: GP-PDE domain-containing protein
BBB: GP-PDE domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8636
Polymers53,2882
Non-polymers5754
Water11,674648
1
AAA: GP-PDE domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9323
Polymers26,6441
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: GP-PDE domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9323
Polymers26,6441
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.130, 43.334, 98.982
Angle α, β, γ (deg.)90.000, 94.084, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein GP-PDE domain-containing protein


Mass: 26644.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage K (virus) / Gene: 812_115, 812a_115, 812F1_115, K1/420_115, K1_115 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U1WFD7
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 3 / Details: 15% (w/v) PEG 8000, 83 mM MES-NaOH, 10 mM Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.52→62.38 Å / Num. obs: 95840 / % possible obs: 95.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.042 / Rrim(I) all: 0.076 / Χ2: 0.79 / Net I/σ(I): 8.4
Reflection shellResolution: 1.52→1.6 Å / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 13737 / CC1/2: 0.652 / Rpim(I) all: 0.466 / Rrim(I) all: 0.802 / Χ2: 0.55

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→62.38 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.822 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2131 4666 4.869 %
Rwork0.1881 91166 -
all0.189 --
obs-95832 95.309 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.003 Å2
Baniso -1Baniso -2Baniso -3
1-0.392 Å2-0 Å20.743 Å2
2---0.542 Å20 Å2
3---0.043 Å2
Refinement stepCycle: LAST / Resolution: 1.52→62.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 36 648 4408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133891
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153660
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.6455271
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5818487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6655489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44824.118187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82415708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4361512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
X-RAY DIFFRACTIONr_nbd_refined0.1940.2675
X-RAY DIFFRACTIONr_symmetry_nbd_other0.160.23276
X-RAY DIFFRACTIONr_nbtor_refined0.160.21846
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2425
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3230.29
X-RAY DIFFRACTIONr_nbd_other0.1240.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.235
X-RAY DIFFRACTIONr_mcbond_it1.3952.2251894
X-RAY DIFFRACTIONr_mcbond_other1.3942.2231893
X-RAY DIFFRACTIONr_mcangle_it2.163.3342370
X-RAY DIFFRACTIONr_mcangle_other2.163.3362371
X-RAY DIFFRACTIONr_scbond_it2.0712.5481997
X-RAY DIFFRACTIONr_scbond_other2.0712.551998
X-RAY DIFFRACTIONr_scangle_it3.2763.7052889
X-RAY DIFFRACTIONr_scangle_other3.2753.7062890
X-RAY DIFFRACTIONr_lrange_it5.47428.5264441
X-RAY DIFFRACTIONr_lrange_other5.21927.3534269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.5550.3233230.3216506X-RAY DIFFRACTION92.2589
1.555-1.5980.2843440.2866563X-RAY DIFFRACTION95.8906
1.598-1.6440.2642980.2546440X-RAY DIFFRACTION96.6992
1.644-1.6950.2593260.2436219X-RAY DIFFRACTION96.1369
1.695-1.750.2773190.2356067X-RAY DIFFRACTION96.4944
1.75-1.8120.2462870.225816X-RAY DIFFRACTION95.3147
1.812-1.880.2332600.2185533X-RAY DIFFRACTION94.4562
1.88-1.9570.2162960.1995447X-RAY DIFFRACTION96.6998
1.957-2.0440.2282530.1885201X-RAY DIFFRACTION95.8019
2.044-2.1430.2122400.1844972X-RAY DIFFRACTION95.7384
2.143-2.2590.222700.1884691X-RAY DIFFRACTION95.2573
2.259-2.3960.2182120.1764327X-RAY DIFFRACTION92.2561
2.396-2.5610.2052080.1714243X-RAY DIFFRACTION96.1962
2.561-2.7670.1911860.1673896X-RAY DIFFRACTION95.2848
2.767-3.030.2012380.1763571X-RAY DIFFRACTION95.2965
3.03-3.3880.2141720.183179X-RAY DIFFRACTION92.4669
3.388-3.9110.2011220.1732952X-RAY DIFFRACTION96.3033
3.911-4.7880.1651500.1542488X-RAY DIFFRACTION96.5947
4.788-6.7630.219930.1961916X-RAY DIFFRACTION94.3636
6.763-62.380.229690.1911139X-RAY DIFFRACTION98.5318

+
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://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