[English] 日本語
Yorodumi
- PDB-4azn: Murine epidermal fatty acid-binding protein (FABP5), apo form, po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4azn
TitleMurine epidermal fatty acid-binding protein (FABP5), apo form, poly- his tag-mediated crystal packing
ComponentsFATTY ACID-BINDING PROTEIN, EPIDERMAL
KeywordsLIPID BINDING PROTEIN / LIPID CARRIER PROTEIN / ENDOCANNABINOID / BETA-BARREL / BETA-CLAMSHELL / DOMAIN SWAPPING
Function / homology
Function and homology information


Signaling by Retinoic Acid / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / lipid transport across blood-brain barrier / retrograde trans-synaptic signaling by endocannabinoid / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process ...Signaling by Retinoic Acid / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / lipid transport across blood-brain barrier / retrograde trans-synaptic signaling by endocannabinoid / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / long-chain fatty acid transmembrane transporter activity / postsynaptic cytosol / postsynaptic density, intracellular component / Neutrophil degranulation / fatty acid binding / lipid metabolic process / glucose metabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / synapse / glutamatergic synapse / extracellular space / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein 5 / Fatty acid binding protein 5, epidermal
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsSanson, B. / Wang, T. / Sun, J. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystallographic Study of Fabp5 as an Intracellular Endocannabinoid Transporter.
Authors: Sanson, B. / Wang, T. / Sun, J. / Wang, L. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H.
History
DepositionJun 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FATTY ACID-BINDING PROTEIN, EPIDERMAL
B: FATTY ACID-BINDING PROTEIN, EPIDERMAL


Theoretical massNumber of molelcules
Total (without water)34,6882
Polymers34,6882
Non-polymers00
Water1,47782
1
A: FATTY ACID-BINDING PROTEIN, EPIDERMAL


Theoretical massNumber of molelcules
Total (without water)17,3441
Polymers17,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FATTY ACID-BINDING PROTEIN, EPIDERMAL


Theoretical massNumber of molelcules
Total (without water)17,3441
Polymers17,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.290, 64.970, 60.100
Angle α, β, γ (deg.)90.00, 122.34, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein FATTY ACID-BINDING PROTEIN, EPIDERMAL / MCG1638 / FABP5 / EPIDERMAL-TYPE FATTY ACID- BINDING PROTEIN / E-FABP / PSORIASIS-ASSOCIATED FATTY ...MCG1638 / FABP5 / EPIDERMAL-TYPE FATTY ACID- BINDING PROTEIN / E-FABP / PSORIASIS-ASSOCIATED FATTY ACID- BINDING PROTEIN HOMOLOG / PA-FABP


Mass: 17343.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Tissue: EPIDERMIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q497I3, UniProt: Q05816*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3350, 100 MM BIS-TRIS PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. CRYPROTECION: 25% GLYCEROL IN MOTHER LIQUOR.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2010
RadiationMonochromator: DOUBLE SILICON(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 10427 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 48.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.2 / % possible all: 62

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B56

1b56


Resolution: 2.51→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.868 / SU B: 26.57 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.814 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28186 521 5 %RANDOM
Rwork0.21437 ---
obs0.21779 9888 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.625 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å21.08 Å2
2---1.33 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 0 82 2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222162
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9552904
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1425.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53115436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3681510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021550
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5451.51352
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04222184
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7463810
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9114.5716
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.574 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 26 -
Rwork0.204 499 -
obs--67.74 %
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)
11.43310.637-0.14764.37360.4262.8993-0.09050.1121-0.0745-0.19380.0369-0.407-0.0170.18360.05360.23140.00680.0830.093-0.02040.121611.927131.609125.5368
24.30461.23490.34574.9334-0.31723.73910.0372-0.240.25130.35570.00630.0012-0.07470.1084-0.04350.2869-0.00680.07120.0297-0.02680.101110.860133.145932.8061
31.78480.064-0.82814.28071.2872.6460.04830.0719-0.0291-0.1869-0.09140.1680.0009-0.12920.04320.1786-0.02040.09650.09730.01940.193422.812520.3654-3.3711
45.49440.29-0.25464.44041.73845.26310.01820.0595-0.08640.1932-0.07160.39540.4357-0.30840.05330.2259-0.0290.12510.0148-0.01420.237416.671918.78320.9734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 79
2X-RAY DIFFRACTION2A80 - 134
3X-RAY DIFFRACTION3B-1 - 79
4X-RAY DIFFRACTION4B80 - 134

+
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