[English] 日本語
Yorodumi
- PDB-4xcp: Fatty Acid and Retinol binding protein Na-FAR-1 from Necator amer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xcp
TitleFatty Acid and Retinol binding protein Na-FAR-1 from Necator americanus
ComponentsNematode fatty acid retinoid binding protein
Keywordsretinol-binding protein / Fatty acid retinol binding
Function / homologyNematode fatty acid retinoid binding / Nematode fatty acid retinoid binding protein (Gp-FAR-1) / lipid binding / extracellular region / PALMITIC ACID / Nematode fatty acid retinoid binding protein
Function and homology information
Biological speciesNecator americanus (New World hookworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsGabrielsen, M. / Rey-Burusco, M.F. / Ibanez-Shimabukuro, M. / Griffiths, K. / Kennedy, M.W. / Corsico, B. / Smith, B.O.
Funding support United Kingdom, Argentina, 3items
OrganizationGrant numberCountry
Wellcome Trust083625 United Kingdom
National Research Council of Argentina Argentina
Biotechnology and Biological Sciences Research CouncilBB/G011389/1 United Kingdom
CitationJournal: Biochem.J. / Year: 2015
Title: Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus.
Authors: Rey-Burusco, M.F. / Ibanez-Shimabukuro, M. / Gabrielsen, M. / Franchini, G.R. / Roe, A.J. / Griffiths, K. / Zhan, B. / Cooper, A. / Kennedy, M.W. / Corsico, B. / Smith, B.O.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nematode fatty acid retinoid binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5513
Polymers19,0381
Non-polymers5132
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint5 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.123, 121.123, 121.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

-
Components

#1: Protein Nematode fatty acid retinoid binding protein


Mass: 19038.008 Da / Num. of mol.: 1 / Fragment: UNP residues 21-175 / Mutation: M1MSE, M15MSE, M70MSE, M115MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Necator americanus (New World hookworm)
Gene: NECAME_14208 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: W2SRJ3
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.48 Å3/Da / Density % sol: 72.53 % / Description: Cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 38 % PEG 300, 100 mM phosphate citrate pH 4.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.14→29.38 Å / Num. all: 17353 / Num. obs: 17353 / % possible obs: 99.91 % / Redundancy: 28.9 % / Biso Wilson estimate: 30.11 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 25.5
Reflection shellResolution: 2.14→2.27 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 4.2 / % possible all: 97

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→29.38 Å / Cor.coef. Fo:Fc: 0.9252 / Cor.coef. Fo:Fc free: 0.9201 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 877 5.06 %RANDOM
Rwork0.203 ---
obs0.2039 17346 99.91 %-
Displacement parametersBiso mean: 32.54 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.273 Å
Refinement stepCycle: LAST / Resolution: 2.14→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 36 136 1385
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011302HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.931765HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d481SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes178HARMONIC5
X-RAY DIFFRACTIONt_it1302HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion18.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion155SEMIHARMONIC5
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_contact1631SEMIHARMONIC4
LS refinement shellResolution: 2.14→2.27 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2502 155 5.72 %
Rwork0.1861 2553 -
all0.1898 2708 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 39.7537 Å / Origin y: 30.7686 Å / Origin z: 11.0724 Å
111213212223313233
T-0.0502 Å20.0237 Å20.0188 Å2-0.0244 Å20.0215 Å2---0.0589 Å2
L0.864 °2-0.1051 °2-0.816 °2-0.5911 °20.0762 °2--1.1149 °2
S-0.0605 Å °-0.0178 Å °-0.0247 Å °-0.0181 Å °0.0712 Å °-0.02 Å °0.007 Å °0.1787 Å °-0.0107 Å °
Refinement TLS groupSelection details: { A|* }

+
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