[English] 日本語
Yorodumi
- PDB-7fy1: Crystal Structure of apo human FABP9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fy1
TitleCrystal Structure of apo human FABP9
ComponentsFatty acid-binding protein 9
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / nucleus / cytosol
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
Similarity search - Domain/homology
MYRISTIC ACID / Fatty acid-binding protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands.
Authors: Ehler, A. / Bartelmus, C. / Benz, J. / Plitzko, I. / 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
Revision 1.2Aug 13, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid-binding protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6242
Polymers15,3961
Non-polymers2281
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.980, 107.980, 76.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Fatty acid-binding protein 9 / Testis lipid-binding protein / TLBP / Testis-type fatty acid-binding protein / T-FABP


Mass: 15395.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP9 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0Z7S8
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.75 %
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: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→46.76 Å / Num. obs: 18103 / % possible obs: 99.7 % / Redundancy: 35.999 % / Biso Wilson estimate: 50.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.078 / Χ2: 0.848 / Net I/σ(I): 23.84 / Num. measured all: 651695 / Scaling rejects: 55
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
2.01-2.0613.2589.9950.316838130012700.13811.45697.7
2.06-2.1236.6414.2071.2646791128112770.6714.26599.7
2.12-2.1839.882.6792.1249691124712460.8012.71499.9
2.18-2.2539.3641.8963.1347827121812150.9041.9299.8
2.25-2.3237.9551.4534.0244331116911680.9251.47299.9
2.32-2.437.5470.9745.8343066114911470.9770.98799.8
2.4-2.4940.3790.6698.4944013109210900.9840.67799.8
2.49-2.5939.9580.4811.5642355106110600.9910.48699.9
2.59-2.7139.1130.35414.9939778102010170.9960.35999.7
2.71-2.8437.0850.25219.67363439849800.9970.25599.6
2.84-338.180.16728356989359350.9980.169100
3-3.1839.6260.12336.35352678908900.9990.125100
3.18-3.438.2390.07849.3321218408400.9990.079100
3.4-3.6735.8140.06557.52829379079010.065100
3.67-4.0235.80.05962.62595572672510.05999.9
4.02-4.4936.7890.04868.952457566966810.04999.9
4.49-5.1935.0070.04569.262079459459410.046100
5.19-6.3632.9730.04864.641704751751710.048100
6.36-8.9933.6010.04867.751391141441410.048100
8.99-46.7626.9270.04362.6700126426010.04498.5

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.01→46.76 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.89 / Stereochemistry target values: ML
Details: loop with Phe56 at exit of ligand binding site has at least two conformations. mixture of fatty acids bound with one being shorter than the other, modeled by reducing occupancy of two ...Details: loop with Phe56 at exit of ligand binding site has at least two conformations. mixture of fatty acids bound with one being shorter than the other, modeled by reducing occupancy of two terminal CH2 to 0.5. data merged from two crystals since refines better than individual models.
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 784 5.05 %RANDOM
Rwork0.2203 14739 --
obs0.2223 15523 85.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.6 Å2 / Biso mean: 67.0738 Å2 / Biso min: 39.08 Å2
Refinement stepCycle: final / Resolution: 2.01→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1069 0 16 13 1098
Biso mean--66.23 53.74 -
Num. residues----134
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.140.3297590.34951101034
2.14-2.30.36411160.30612207232379
2.3-2.530.31411460.292328142960100
2.53-2.90.33271600.304728322992100
2.9-3.650.29471400.240428893029100
3.65-46.760.20891630.173430463209100
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)
13.10820.85220.15665.2508-1.62553.85050.12691.26340.16910.0747-0.6102-0.85620.82430.68990.37130.7980.1160.24560.518-0.01260.5062-43.355814.5733-10.6342
21.9309-2.7263-1.3894.08471.7092.86280.1349-0.53630.95120.21340.01910.1621-1.44440.3711-0.30280.7287-0.05590.32180.5047-0.11380.6388-60.429323.9141.4729
33.53412.3059-0.20282.15150.73343.77611.1625-0.99490.87642.0313-1.1854-0.6886-1.29791.34840.01681.1205-0.32870.25260.38650.0070.6591-41.738818.736-0.2172
42.89240.19030.77626.9572-0.85264.07030.49210.0450.20940.2374-0.43330.09310.5044-0.0361-0.08830.6559-0.08960.11240.2543-0.03780.3334-51.32211.3266-2.0054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 15 )A-1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 35 )A16 - 35
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 65 )A36 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 132 )A66 - 132

+
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