[English] 日本語
Yorodumi
- PDB-7g0w: Crystal Structure of apo human FABP1i monoclinic form II, twinned... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7g0w
TitleCrystal Structure of apo human FABP1i monoclinic form II, twinned with beta=90deg
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
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 / Heme degradation / long-chain fatty acid transmembrane transporter activity / 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 / Heme degradation / long-chain fatty acid transmembrane transporter activity / 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
Similarity search - Domain/homology
BENZAMIDINE / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human FABP1 complex
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,1906
Polymers58,0354
Non-polymers1562
Water7,999444
1
A: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,5091
Polymers14,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,5091
Polymers14,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6643
Polymers14,5091
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)14,5091
Polymers14,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.947, 106.685, 56.261
Angle α, β, γ (deg.)90.000, 90.360, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 14508.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07148
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.01 Å3/Da / Density % sol: 38.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.22
ReflectionResolution: 1.64→38.71 Å / Num. obs: 56090 / % possible obs: 99.8 % / Redundancy: 3.32 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.064 / Rsym value: 0.056 / Χ2: 0.884 / Net I/σ(I): 12.22 / Num. measured all: 184675 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.64-1.683.1531.0621.2113079417541480.3341.27799.4
1.68-1.733.1010.811.5712305399739680.4640.97799.3
1.73-1.782.990.6251.9811752397639300.5930.76298.8
1.78-1.833.3760.4592.9112673379237540.7250.54599
1.83-1.893.4160.3483.9712573369936810.8240.41399.5
1.89-1.963.380.2415.8112050358135650.9060.28799.6
1.96-2.033.3160.1787.4511375344034300.9430.21399.7
2.03-2.123.130.1418.9710365332933120.9520.17199.5
2.12-2.213.440.1111.7610939319131800.9740.13199.7
2.21-2.323.4870.09213.910640305830510.9820.10999.8
2.32-2.443.4570.07616.3410076291929150.9880.0999.9
2.44-2.593.3950.0619.139298274827390.9910.07299.7
2.59-2.773.1480.05121.658055256525590.9930.06199.8
2.77-2.993.5720.04127.898637242324180.9960.04899.8
2.99-3.283.4740.03432.667615219521920.9970.0499.9
3.28-3.673.3250.03136.696556199319720.9970.03898.9
3.67-4.233.1250.02937.535568179517820.9970.03499.3
4.23-5.193.4970.02641.885172149014790.9980.03199.3
5.19-7.333.2360.02639.13741116611560.9980.03199.1
7.33-38.7093.3470.02741.7222066666590.9990.03298.9

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_989refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.64→38.709 Å / FOM work R set: 0.7413 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.87 / Stereochemistry target values: TWIN_LSQ_F
Details: twin law -H,-K,L benzamidine at surface from crystallization conditions
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 2845 5.08 %RANDOM
Rwork0.1771 53198 --
obs0.1791 56050 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.653 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 56.86 Å2 / Biso mean: 25.65 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.3499 Å2-0 Å2-0.1634 Å2
2--0.6789 Å2-0 Å2
3---0.671 Å2
Refinement stepCycle: final / Resolution: 1.64→38.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 10 444 4466
Biso mean--31.08 28.73 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074096
X-RAY DIFFRACTIONf_angle_d1.0225485
X-RAY DIFFRACTIONf_chiral_restr0.068641
X-RAY DIFFRACTIONf_plane_restr0.003697
X-RAY DIFFRACTIONf_dihedral_angle_d16.021569
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6401-1.66830.3551600.33462671283194
1.6683-1.69870.29731350.3212666280195
1.6987-1.73130.31851250.32162615274095
1.7313-1.76670.3551430.31882674281795
1.7667-1.80510.34971320.29662665279795
1.8051-1.8470.28881410.28742649279095
1.847-1.89320.30611530.26722617277094
1.8932-1.94440.33461300.25112695282595
1.9444-2.00160.27761650.24272603276894
2.0016-2.06620.25011210.2312658277995
2.0662-2.140.25181370.21322680281795
2.14-2.22560.2361410.20652628276995
2.2256-2.32680.26131440.20172650279495
2.3268-2.44940.21581600.19532670283094
2.4494-2.60270.24751520.19152650280295
2.6027-2.80340.22361340.18082680281495
2.8034-3.0850.23221320.15972667279995
3.085-3.53040.19191420.13012678282095
3.5304-4.44380.16091530.10682658281195
4.4438-24.8850.15451370.12142724286195

+
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