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- PDB-7fy1: Crystal Structure of apo human FABP9 -

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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: To be published
Title: Crystal Structure of apo human FABP9
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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