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- PDB-9m2b: X-ray structure of human heart fatty acid-binding protein (apo-FABP3) -

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Basic information

Entry
Database: PDB / ID: 9m2b
TitleX-ray structure of human heart fatty acid-binding protein (apo-FABP3)
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP3 / apo / binding protein / fatty acid
Function / homology
Function and homology information


icosatetraenoic acid binding / positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / oleic acid binding / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / response to fatty acid / phospholipid homeostasis / long-chain fatty acid transmembrane transporter activity ...icosatetraenoic acid binding / positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / oleic acid binding / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / response to fatty acid / phospholipid homeostasis / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / Triglyceride catabolism / sarcoplasm / long-chain fatty acid transport / cytoskeletal protein binding / brown fat cell differentiation / cholesterol homeostasis / fatty acid metabolic process / response to insulin / response to xenobiotic stimulus / negative regulation of cell population proliferation / : / 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
ACETIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsSugiyama, S. / Maekawa, S. / Matsuoka, S. / Murata, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)23ak0101198h0001 Japan
Japan Society for the Promotion of Science (JSPS)23K17373 Japan
Japan Science and TechnologyJPMJER1005 Japan
CitationJournal: To Be Published
Title: X-ray structure of human heart fatty acid-binding protein (apo-FABP3)
Authors: Sugiyama, S. / Maekawa, S. / Matsuoka, S. / Murata, M.
History
DepositionFeb 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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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)29,8784
Polymers29,7582
Non-polymers1202
Water7,674426
1
A: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9392
Polymers14,8791
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9392
Polymers14,8791
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.576, 27.912, 58.403
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211

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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: 14879.022 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli (E. coli) / References: UniProt: P05413
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES-NaOH(pH6.0), 30% PEG 3350, 3% Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.18→70.48 Å / Num. obs: 71921 / % possible obs: 95.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.1
Reflection shellResolution: 1.18→1.2 Å / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2 / Num. unique obs: 3527

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→29.52 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.846 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18808 3673 5.1 %RANDOM
Rwork0.14645 ---
obs0.1486 68236 95.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.08 Å2
2---0.68 Å2-0 Å2
3---1.35 Å2
Refinement stepCycle: 1 / Resolution: 1.18→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 8 426 2522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132411
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172321
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.6493284
X-RAY DIFFRACTIONr_angle_other_deg1.5211.5925420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46124.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57315474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.165158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022745
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02475
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_it2.5041.3241219
X-RAY DIFFRACTIONr_mcbond_other2.5041.3251217
X-RAY DIFFRACTIONr_mcangle_it3.2281.9961558
X-RAY DIFFRACTIONr_mcangle_other3.2271.9951559
X-RAY DIFFRACTIONr_scbond_it2.9481.6281192
X-RAY DIFFRACTIONr_scbond_other2.9471.6281193
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8942.3271727
X-RAY DIFFRACTIONr_long_range_B_refined5.91118.2152738
X-RAY DIFFRACTIONr_long_range_B_other4.9916.8812598
X-RAY DIFFRACTIONr_rigid_bond_restr5.00634732
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.181→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 263 -
Rwork0.246 4831 -
obs--91.14 %

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