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- PDB-3rsw: Crystal Structure of Heart Fatty Acid Binding Protein (FABP3) -

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Basic information

Entry
Database: PDB / ID: 3rsw
TitleCrystal Structure of Heart Fatty Acid Binding Protein (FABP3)
ComponentsFatty acid-binding protein, heart
KeywordsCHAPERONE / Lipid carrier / molecular chaperone / Heart Fatty Acid Binding Protein / Type 2 diabetes / atherosclerosis
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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsCarney, D.F. / Shankaran, B. / Zwart, P.H. / Stebbins, J.W. / Prasad, G.S.
CitationJournal: To be Published
Title: Crystal Structure of Heart Fatty Acid Binding Protein (FABP3)
Authors: Carney, D.F. / Shankaran, B. / Zwart, P.H. / Stebbins, J.W. / Prasad, G.S.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)35,3022
Polymers35,3022
Non-polymers00
Water66737
1
A: Fatty acid-binding protein, heart


Theoretical massNumber of molelcules
Total (without water)17,6511
Polymers17,6511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, heart


Theoretical massNumber of molelcules
Total (without water)17,6511
Polymers17,6511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.472, 42.472, 168.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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: 17651.123 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 (E. coli) / Strain (production host): BL21 / References: UniProt: P05413
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.2
Details: 0.1M Citric Acid, pH 3.2 and 32% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.513
11K, H, -L20.487
ReflectionResolution: 2.599→84.4 Å / Num. all: 9216 / Num. obs: 9216 / % possible obs: 99.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 11.4 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.167 / Rsym value: 0.167 / Net I/σ(I): 11.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.599→42.48 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.896 / SU B: 20.78 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27306 395 4.3 %RANDOM
Rwork0.22615 ---
obs0.22829 8785 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.761 Å2
Baniso -1Baniso -2Baniso -3
1-5.47 Å20 Å20 Å2
2--5.47 Å20 Å2
3----10.94 Å2
Refinement stepCycle: LAST / Resolution: 2.599→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 0 37 2123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222116
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.9612854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0315264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.4222584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.76415408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.862158
X-RAY DIFFRACTIONr_chiral_restr0.120.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021496
X-RAY DIFFRACTIONr_mcbond_it0.5921.51310
X-RAY DIFFRACTIONr_mcangle_it1.06722128
X-RAY DIFFRACTIONr_scbond_it1.7473806
X-RAY DIFFRACTIONr_scangle_it2.6884.5726
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 24 -
Rwork0.191 654 -
obs--98.83 %
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)
12.3726-0.29690.81621.10480.13011.311-0.1893-0.2766-0.17560.28790.0927-0.35960.16760.33820.09670.2462-0.01190.00890.40040.03480.23319.7058-10.609410.935
22.46480.13750.55670.9588-0.43121.5085-0.09370.2083-0.0156-0.23320.09160.36940.1117-0.43570.00210.22880.01340.00750.3085-0.01890.2286-9.7084-10.5943-15.1926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 133
2X-RAY DIFFRACTION2B1 - 133

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