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- PDB-7fzq: Crystal Structure of human FABP3 in complex with myristate -

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Basic information

Entry
Database: PDB / ID: 7fzq
TitleCrystal Structure of human FABP3 in complex with myristate
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport ...positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / negative regulation of cell population proliferation / extracellular space / extracellular exosome / 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 / NICKEL (II) ION / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.597 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 human FABP3 in complex with myristate
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,6685
Polymers30,3232
Non-polymers3463
Water4,107228
1
A: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4483
Polymers15,1611
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2202
Polymers15,1611
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.852, 29.864, 81.060
Angle α, β, γ (deg.)90.000, 122.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fatty acid-binding protein, heart / Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived ...Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived growth inhibitor / MDGI / Muscle fatty acid-binding protein / M-FABP


Mass: 15161.298 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05413
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-MYR / MYRISTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
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: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.597→35.45 Å / Num. obs: 36682 / % possible obs: 98.4 % / Redundancy: 3.267 % / Biso Wilson estimate: 14.45 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.114 / Χ2: 0.915 / Net I/σ(I): 8.53 / Num. measured all: 99576 / Scaling rejects: 77
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
1.597-1.742.9940.5871.716317226721100.7490.70993.1
1.74-1.793.1950.4822.146940218121720.8450.57999.6
1.79-1.843.4340.3972.737414216521590.8750.4799.7
1.84-1.93.4140.4382.57047207920640.890.51999.3
1.9-1.963.4080.3143.936769201819860.9070.37298.4
1.96-2.033.3180.2284.736436195619400.9540.27299.2
2.03-2.13.1540.1965.625898188718700.9510.23699.1
2.1-2.193.3290.1766.296128184918410.9630.2199.6
2.19-2.293.3830.1816.775808175017170.9580.21598.1
2.29-2.43.4070.1428.045598165716430.9730.16999.2
2.4-2.533.320.111105316161416010.9810.13399.2
2.53-2.683.1320.09311.454663150514890.9840.11298.9
2.68-2.873.260.08413.174567141814010.9860.10198.8
2.87-3.13.3660.067164437134013180.9920.0898.4
3.1-3.393.2670.05418.783976124312170.9940.06597.9
3.39-3.793.0570.05518.423332111410900.9940.06797.8
3.79-4.383.0350.04420.69299610099870.9960.05297.8
4.38-5.373.3250.0423.1227438408250.9970.04798.2
5.37-7.593.0150.04219.8520146796680.9950.05198.4
7.59-35.4453.0890.03322.611773973810.9980.03996

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.597→35.445 Å / FOM work R set: 0.7347 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 32.63 / Stereochemistry target values: ML
Details: only one molecule in a.u. has fatty acid bound, the other is empty
RfactorNum. reflection% reflectionSelection details
Rfree0.2935 1719 5.1 %RANDOM
Rwork0.2516 31964 --
obs0.2538 33683 91.37 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.905 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 77.56 Å2 / Biso mean: 20.7 Å2 / Biso min: 6.79 Å2
Baniso -1Baniso -2Baniso -3
1--5.8823 Å2-0 Å2-3.3397 Å2
2---1.6841 Å20 Å2
3---7.5663 Å2
Refinement stepCycle: final / Resolution: 1.597→35.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 18 228 2360
Biso mean--25.3 25.39 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072167
X-RAY DIFFRACTIONf_angle_d1.0122920
X-RAY DIFFRACTIONf_chiral_restr0.064349
X-RAY DIFFRACTIONf_plane_restr0.003360
X-RAY DIFFRACTIONf_dihedral_angle_d13.751801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5973-1.64430.39481320.36232265239779
1.6443-1.69730.39351460.32992361250783
1.6973-1.7580.361370.30322505264286
1.758-1.82840.36251430.28592526266989
1.8284-1.91160.33081070.27992444255184
1.9116-2.01240.33011290.28332664279391
2.0124-2.13840.3391250.26172802292796
2.1384-2.30350.33111520.27592680283292
2.3035-2.53530.28921600.24922846300698
2.5353-2.9020.28961600.24032889304999
2.902-3.65560.28531490.23482953310299
3.6556-35.45410.22061790.210630293208100
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)
10.3438-0.27020.27880.2451-0.15380.352-0.00860.0065-0.01760.0044-0.05130.0170.01760.04150.04210.0703-0.0032-0.01380.08380.01180.0851-18.53120.92620.3288
20.9237-0.26270.14770.19740.06240.2344-0.02470.0917-0.1424-0.0189-0.0190.0467-0.0410.06040.03250.0809-0.0079-0.00870.0790.0160.0956-2.9227-6.581132.3021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-2 - 131
2X-RAY DIFFRACTION2chain BB-3 - 131

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