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- PDB-3wbg: Structure of the human heart fatty acid-binding protein in comple... -

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Basic information

Entry
Database: PDB / ID: 3wbg
TitleStructure of the human heart fatty acid-binding protein in complex with 1-anilinonaphtalene-8-sulphonic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / beta barrel
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
8-ANILINO-1-NAPHTHALENE SULFONATE / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsHirose, M. / Sugiyama, S. / Ishida, H. / Niiyama, M. / Matsuoka, D. / Hara, T. / Sato, F. / Mizohata, E. / Murakami, S. / Inoue, T. ...Hirose, M. / Sugiyama, S. / Ishida, H. / Niiyama, M. / Matsuoka, D. / Hara, T. / Sato, F. / Mizohata, E. / Murakami, S. / Inoue, T. / Matsuoka, S. / Murata, M.
CitationJournal: J.SYNCHROTRON RADIAT. / Year: 2013
Title: Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilinonaphthalene-8-sulphonic acid
Authors: Hirose, M. / Sugiyama, S. / Ishida, H. / Niiyama, M. / Matsuoka, D. / Hara, T. / Mizohata, E. / Murakami, S. / Inoue, T. / Matsuoka, S. / Murata, M.
History
DepositionMay 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,3998
Polymers68,2024
Non-polymers1,1974
Water3,135174
1
A: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3502
Polymers17,0501
Non-polymers2991
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)17,3502
Polymers17,0501
Non-polymers2991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3502
Polymers17,0501
Non-polymers2991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3502
Polymers17,0501
Non-polymers2991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.157, 29.359, 140.689
Angle α, β, γ (deg.)90.000, 112.470, 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: 17050.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05413
#2: Chemical
ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE / 8-Anilinonaphthalene-1-sulfonic acid


Mass: 299.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H13NO3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM MES, 30% PEG3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL38B120.9
Detector
TypeIDDetector
RAYONIX MX-2251CCD
RAYONIX MX-2252CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 24494 / % possible obs: 90 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.47 Å29.85 Å
Translation2.47 Å29.85 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→29.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.114 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.452 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2912 1220 5 %RANDOM
Rwork0.2176 ---
obs0.2214 24208 89.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.43 Å2 / Biso mean: 29.0587 Å2 / Biso min: 10.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.02 Å2
2--0.05 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 84 174 4410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224323
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.9855841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.71225.059170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5615819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0391516
X-RAY DIFFRACTIONr_chiral_restr0.1110.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023076
X-RAY DIFFRACTIONr_mcbond_it0.9171.52620
X-RAY DIFFRACTIONr_mcangle_it1.67724266
X-RAY DIFFRACTIONr_scbond_it2.55531703
X-RAY DIFFRACTIONr_scangle_it3.8554.51575
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 76 -
Rwork0.272 1679 -
all-1755 -
obs--90 %

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