[English] 日本語
Yorodumi
- PDB-6i8x: As-p18, an extracellular fatty acid binding protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i8x
TitleAs-p18, an extracellular fatty acid binding protein
ComponentsFatty acid-binding protein homolog
KeywordsLIPID BINDING PROTEIN / Extracellular / nematodes / fatty acid binding
Function / homology
Function and homology information


Fatty acid-binding protein homologue 1/2/3/4 / Cytosolic fatty-acid binding proteins signature. / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
VACCENIC ACID / Fatty acid-binding protein homolog
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGabrielsen, M. / Riboldi-Tunnicliffe, A. / Ibanez-Shimabukuro, M. / Smith, B.O.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust083625 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/G011389/1 United Kingdom
Citation
Journal: Biosci.Rep. / Year: 2019
Title: As-p18, an extracellular fatty acid binding protein of nematodes, exhibits unusual structural features.
Authors: Ibanez-Shimabukuro, M. / Rey-Burusco, M.F. / Gabrielsen, M. / Franchini, G.R. / Riboldi-Tunnicliffe, A. / Roe, A.J. / Griffiths, K. / Cooper, A. / Corsico, B. / Kennedy, M.W. / Smith, B.O.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012
Title: Useable diffraction data from a multiple microdomain-containing crystal of Ascaris suum As-p18 fatty-acid-binding protein using a microfocus beamline.
Authors: Gabrielsen, M. / Riboldi-Tunnicliffe, A. / Ibanez-Shimabukuro, M. / Griffiths, K. / Roe, A.J. / Cooper, A. / Smith, B.O. / Corsico, B. / Kennedy, M.W.
History
DepositionNov 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid-binding protein homolog
B: Fatty acid-binding protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,66314
Polymers35,2762
Non-polymers1,38812
Water1,928107
1
A: Fatty acid-binding protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,68111
Polymers17,6381
Non-polymers1,04310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9823
Polymers17,6381
Non-polymers3452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.254, 102.254, 103.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Fatty acid-binding protein homolog / AS-P18


Mass: 17637.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P55776
#2: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.97 Å3/Da / Density % sol: 69.03 % / Description: Square cuboid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 40% ethylene glycol, 0.1 M acetate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.3→20.06 Å / Num. obs: 23648 / % possible obs: 93.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.52 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.104 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Rpim(I) all: 0.435 / Rrim(I) all: 0.679 / % possible all: 77.1

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G74

1g74


Resolution: 2.3→14.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.184 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1199 5.16 %RANDOM
Rwork0.179 ---
obs0.181 23252 98.6 %-
Displacement parametersBiso mean: 47.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.0353 Å20 Å20 Å2
2---1.0353 Å20 Å2
3---2.0706 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.3→14.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 94 107 2637
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012733HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073775HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d987SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes362HARMONIC5
X-RAY DIFFRACTIONt_it2733HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion19.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion312SEMIHARMONIC5
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_contact2815SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.234 155 5.99 %
Rwork0.217 2432 -
all0.218 2587 -
obs--89.05 %
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)
12.441-0.01380.75680.5378-0.22161.5142-0.0517-0.11150.18340.05470.01420.0276-0.21530.00960.0375-0.0113-0.0243-0.0025-0.0491-0.0544-0.10356.959726.525856.8608
21.6433-0.52670.0731.01680.21931.81270.06980.09970.1328-0.1682-0.0338-0.0439-0.28880.0549-0.0360.0068-0.03870.0382-0.05780.053-0.119414.391322.807229.0953
31.52221.7040.48772.9827-0.29041.80570.0104-0.0676-0.0314-0.0354-0.0133-0.0080.0509-0.07760.00290.1722-0.0672-0.06330.14590.00680.19219.633122.890242.5412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

+
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