[English] 日本語
Yorodumi
- PDB-5ijm: Crystal Structure of an Acyl-CoA Binding Protein (LmjF.17.0620) o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ijm
TitleCrystal Structure of an Acyl-CoA Binding Protein (LmjF.17.0620) of Leishmania major
ComponentsUncharacterized protein
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


fatty-acyl-CoA binding / ciliary plasm / fatty acid metabolic process / nucleoplasm / cytoplasm
Similarity search - Function
Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / FERM/acyl-CoA-binding protein superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACB domain-containing protein
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsDangi, R.S. / Pal, R.K. / Sundd, M.
CitationJournal: To Be Published
Title: Crystal Structure of an Acyl-CoA Binding Protein (LmjF.17.0620) of Leishmania major
Authors: Dangi, R.S. / Pal, R.K. / Sundd, M.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,7581
Polymers11,7581
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6380 Å2
Unit cell
Length a, b, c (Å)26.989, 29.076, 33.778
Angle α, β, γ (deg.)103.81, 110.42, 95.00
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Uncharacterized protein / Acyl CoA Binding Protein


Mass: 11758.317 Da / Num. of mol.: 1 / Mutation: E22D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LMJF_17_0620 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4QED2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.02 Å3/Da / Density % sol: 39.09 % / Description: Rod-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M Sodium Citrate tribasic dihydrate, 10%(v/v) 2-Propanol, 20%(w/v) PEG4000
PH range: 5.0-5.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 9, 2014 / Details: Varimax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.46→30.31 Å / Num. obs: 14140 / % possible obs: 88.3 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.022 / Net I/σ(I): 17.62
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 15.98 / % possible all: 73.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FP5

3fp5


Resolution: 1.46→30.31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.947 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17699 707 5 %RANDOM
Rwork0.15983 ---
obs0.16076 13433 89.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0.23 Å20.5 Å2
2---0.6 Å2-0.29 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.46→30.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 0 0 170 921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02786
X-RAY DIFFRACTIONr_bond_other_d0.0040.02728
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.9371071
X-RAY DIFFRACTIONr_angle_other_deg1.13531674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1855103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27323.82434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86715127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.188155
X-RAY DIFFRACTIONr_chiral_restr0.1360.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021907
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02184
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1341.473397
X-RAY DIFFRACTIONr_mcbond_other1.9721.459396
X-RAY DIFFRACTIONr_mcangle_it2.7772.198496
X-RAY DIFFRACTIONr_mcangle_other2.7842.206497
X-RAY DIFFRACTIONr_scbond_it2.9381.717389
X-RAY DIFFRACTIONr_scbond_other2.9351.724390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8082.483573
X-RAY DIFFRACTIONr_long_range_B_refined5.58714.0341091
X-RAY DIFFRACTIONr_long_range_B_other5.2212.7986
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.463→1.501 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 47 -
Rwork0.268 898 -
obs--81.82 %

+
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