[English] 日本語
Yorodumi
- PDB-3b2j: Iodide derivative of human LFABP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b2j
TitleIodide derivative of human LFABP
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / LFABP / Iodide-SAD / Copper Kalpha / Palmitic acid
Function / homology
Function and homology information


response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / long-chain fatty acid transmembrane transporter activity / Heme degradation / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / long-chain fatty acid transmembrane transporter activity / Heme degradation / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / : / Regulation of lipid metabolism by PPARalpha / fatty acid binding / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / PALMITIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo Sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsSharma, A. / Yogavel, M. / Sharma, A.
CitationJournal: J.Struct.Funct.Genom. / Year: 2012
Title: Utility of anion and cation combinations for phasing of protein structures.
Authors: Sharma, A. / Yogavel, M. / Sharma, A.
History
DepositionAug 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8749
Polymers14,6001
Non-polymers1,2748
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.982, 57.608, 75.984
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver-type fatty acid-binding protein / L-FABP


Mass: 14599.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo Sapiens (human) / Gene: FABP1, FABPL / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P07148
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.17 Å3/Da / Density % sol: 43.38 % / Mosaicity: 1.283 °
Crystal growTemperature: 293 K / Method: hanging drop / pH: 8
Details: 30% PEG MME 2000, 0.15M KBr, pH 8.0, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 10, 2009 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 9094 / Num. obs: 9041 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.105 / Χ2: 1.692 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.07120.4588441.387194
2.07-2.1513.70.4178731.3051100
2.15-2.2513.80.3338901.3671100
2.25-2.3713.80.2729061.3411100
2.37-2.5213.80.2348921.4661100
2.52-2.7113.90.1739091.4811100
2.71-2.9913.90.1229011.7011100
2.99-3.4213.70.0869292.2291100
3.42-4.3113.40.0659432.1821100
4.31-5012.40.0610072.375199.7

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→8 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.856 / WRfactor Rfree: 0.2705 / WRfactor Rwork: 0.1965 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8142 / SU B: 5.288 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2672 / SU Rfree: 0.2366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2922 880 9.9 %RANDOM
Rwork0.2063 ---
all0.2145 ---
obs0.2145 8872 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.8 Å2 / Biso mean: 23.9616 Å2 / Biso min: 2.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 42 134 1185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221087
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.9911451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2426.95746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57315220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.568152
X-RAY DIFFRACTIONr_chiral_restr0.0750.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02768
X-RAY DIFFRACTIONr_nbd_refined0.1740.2451
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2708
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.222
X-RAY DIFFRACTIONr_mcbond_it0.4291.5656
X-RAY DIFFRACTIONr_mcangle_it0.81521067
X-RAY DIFFRACTIONr_scbond_it1.2373446
X-RAY DIFFRACTIONr_scangle_it2.2184.5379
LS refinement shellResolution: 2.002→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 70 -
Rwork0.219 529 -
all-599 -
obs--96.93 %

+
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