[English] 日本語
Yorodumi
- PDB-5qhk: PanDDA analysis group deposition of models with modelled events (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5qhk
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human FAM83B in complex with FMOPL000010a
ComponentsProtein FAM83B
KeywordsPROTEIN BINDING / PanDDA / SGC - Diamond I04-1 fragment screening / DUF1669 domain / XChemExplorer
Function / homology
Function and homology information


phosphatidylinositol 3-kinase catalytic subunit binding / phosphatidylinositol 3-kinase regulatory subunit binding / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / Signaling by EGFR / cell population proliferation / protein kinase binding ...phosphatidylinositol 3-kinase catalytic subunit binding / phosphatidylinositol 3-kinase regulatory subunit binding / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / Signaling by EGFR / cell population proliferation / protein kinase binding / signal transduction / membrane / cytosol / cytoplasm
Similarity search - Function
FAM83, N-terminal / : / FAM83 A-H / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
di(piperidin-1-yl)methanone / IODIDE ION / Protein FAM83B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.61 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Fox, A.E. / Talon, R. / Krojer, T. / Douangamath, A. / Collins, P. / Zhang, R. / von Delft, F. / Bountra, C. ...Pinkas, D.M. / Bufton, J.C. / Fox, A.E. / Talon, R. / Krojer, T. / Douangamath, A. / Collins, P. / Zhang, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Bullock, A.N.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)
Authors: Pinkas, D.M. / Bufton, J.C. / Fox, A.E. / Talon, R. / Krojer, T. / Douangamath, A. / Collins, P. / Zhang, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Bullock, A.N.
History
DepositionMay 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein FAM83B
B: Protein FAM83B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,83914
Polymers41,5662
Non-polymers1,27312
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-1 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.380, 74.090, 63.080
Angle α, β, γ (deg.)90.000, 96.190, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein FAM83B


Mass: 20783.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM83B, C6orf143 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T0W9
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOY / di(piperidin-1-yl)methanone


Mass: 196.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.09 Å3/Da / Density % sol: 41.13 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M NaP monobasic, 0.8M KP dibasic, 0.1M HEPES pH 7.5 5%(w/v) PEG10K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.61→33.6 Å / Num. obs: 43891 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.062 / Rrim(I) all: 0.115 / Net I/σ(I): 8.1 / Num. measured all: 145855 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.61-1.651.081097632400.5280.691.2851.299.9
7.2-33.60.02916384790.9980.0180.03432.589.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LZK

5lzk


Resolution: 1.61→62.71 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.902 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 2130 4.9 %RANDOM
Rwork0.1715 ---
obs0.1733 41738 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 197.24 Å2 / Biso mean: 25.093 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å2-0 Å20.15 Å2
2---1.37 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: final / Resolution: 1.61→62.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 56 274 3075
Biso mean--40.85 42.13 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023392
X-RAY DIFFRACTIONr_bond_other_d0.0020.023011
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9634295
X-RAY DIFFRACTIONr_angle_other_deg1.08836993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6025396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74722.746142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96715575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2061526
X-RAY DIFFRACTIONr_chiral_restr0.1290.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02706
X-RAY DIFFRACTIONr_mcbond_it2.0422.1381602
X-RAY DIFFRACTIONr_mcbond_other2.0412.1381603
X-RAY DIFFRACTIONr_mcangle_it2.9613.1861928
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 180 -
Rwork0.319 3051 -
all-3231 -
obs--99.78 %

+
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