[English] 日本語
Yorodumi
- PDB-4fyg: Structural basis for substrate recognition by a novel Legionella ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fyg
TitleStructural basis for substrate recognition by a novel Legionella phosphoinositide phosphatase
ComponentsSidF, inhibitor of growth family, member 3
KeywordsHYDROLASE / mixed alpha-beta / phosphoinositide phosphatase / phosphoinositides / membrane
Function / homology: / Phosphoinositide phosphatase / phosphatidylinositol phosphate phosphatase activity / membrane / Chem-3PT / SidF, inhibitor of growth family, member 3
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.822 Å
AuthorsHsu, F.S. / Zhu, W. / Brennan, L. / Tao, L. / Luo, Z.Q. / Mao, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for substrate recognition by a unique Legionella phosphoinositide phosphatase.
Authors: Hsu, F. / Zhu, W. / Brennan, L. / Tao, L. / Luo, Z.Q. / Mao, Y.
History
DepositionJul 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SidF, inhibitor of growth family, member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8262
Polymers86,1911
Non-polymers6341
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.230, 114.833, 124.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SidF, inhibitor of growth family, member 3 /


Mass: 86191.359 Da / Num. of mol.: 1
Fragment: N-terminal phosphatase domain of SidF (UNP Residues 1-760)
Mutation: C645S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2584, sidF / Plasmid: Pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q5ZSD5, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase
#2: Chemical ChemComp-3PT / (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate


Mass: 634.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H33O19P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl pH8.0, 10% PEG3350, and 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9789 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 4, 2012 / Details: mirrors
RadiationMonochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. all: 301119 / Num. obs: 24387 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 28.6
Reflection shellResolution: 2.82→2.9 Å / % possible all: 78.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4FYF

4fyf


Resolution: 2.822→36.58 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.91 / SU B: 30.281 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 1246 5.1 %RANDOM
Rwork0.17907 ---
obs0.18279 22955 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.396 Å2
Baniso -1Baniso -2Baniso -3
1-4.92 Å20 Å20 Å2
2---4.77 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.822→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5923 0 39 6 5968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026067
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9538179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88925.382314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.045151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3121533
X-RAY DIFFRACTIONr_chiral_restr0.1160.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214609
LS refinement shellResolution: 2.822→2.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 74 -
Rwork0.274 1164 -
obs--71.73 %
Refinement TLS params.Method: refined / Origin x: -2.5584 Å / Origin y: 45.7343 Å / Origin z: 21.9739 Å
111213212223313233
T0.0833 Å2-0.072 Å20.0428 Å2-0.1086 Å2-0.0476 Å2--0.0429 Å2
L1.1072 °2-0.5332 °2-0.4577 °2-2.6096 °20.7847 °2--1.4611 °2
S0.1657 Å °-0.2106 Å °0.1938 Å °-0.2138 Å °-0.0142 Å °-0.0664 Å °-0.1387 Å °-0.0026 Å °-0.1515 Å °

+
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