[English] 日本語
Yorodumi
- PDB-2yoq: Structure of FAM3B PANDER E30 construct -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yoq
TitleStructure of FAM3B PANDER E30 construct
ComponentsPROTEIN FAM3B
KeywordsAPOPTOSIS / DIABETES / ILEI / EMT
Function / homology
Function and homology information


insulin secretion / nuclear envelope lumen / cytokine activity / carbohydrate binding / apoptotic process / extracellular space / extracellular region
Similarity search - Function
FAM3 family / GG-type lectin domain profile. / ILEI/PANDER domain / Interleukin-like EMT inducer
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsJohansson, P. / Bernstrom, J. / Gorman, T. / Oster, L. / Backstrom, S. / Schweikart, F. / Xu, B. / Xue, Y. / Holmberg Schiavone, L.
CitationJournal: Structure / Year: 2013
Title: Fam3B Pander and Fam3C Ilei Represent a Distinct Class of Signaling Molecules with a Non-Cytokine-Like Fold.
Authors: Johansson, P. / Bernstrom, J. / Gorman, T. / Oster, L. / Backstrom, S. / Schweikart, F. / Xu, B. / Xue, Y. / Schiavone, L.H.
History
DepositionOct 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN FAM3B
B: PROTEIN FAM3B
C: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1996
Polymers71,9233
Non-polymers2763
Water7,422412
1
A: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0662
Polymers23,9741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0662
Polymers23,9741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN FAM3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0662
Polymers23,9741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.540, 86.540, 96.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.584, 0.811, -0.016), (0.811, -0.584), (-0.009, -0.013, -1)37.754, -24.817, -76.47
2given(0.401, 0.916, -0.026), (0.916, -0.401, -0.009), (-0.018, -0.02, -1)4.808, -50.132, -75.648

-
Components

#1: Protein PROTEIN FAM3B / CYTOKINE-LIKE PROTEIN 2-21 / PANCREATIC-DERIVED FACTOR / PANDER


Mass: 23974.236 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9D309
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 3.2 Å3/Da / Density % sol: 61.13 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.35→34.47 Å / Num. obs: 33513 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 42.49 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→21.64 Å / Cor.coef. Fo:Fc: 0.9457 / Cor.coef. Fo:Fc free: 0.9344 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.167
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 1690 5.05 %RANDOM
Rwork0.1583 ---
obs0.1599 33459 99.8 %-
Displacement parametersBiso mean: 34.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.1405 Å20 Å20 Å2
2---3.1405 Å20 Å2
3---6.281 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 2.35→21.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 18 412 4706
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014390HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.165902HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1566SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC2
X-RAY DIFFRACTIONt_gen_planes629HARMONIC5
X-RAY DIFFRACTIONt_it4390HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion20.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion554SEMIHARMONIC5
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_contact5052SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.42 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2846 138 4.88 %
Rwork0.2099 2692 -
all0.2135 2830 -
obs--99.8 %

+
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