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- PDB-6ayl: Human adipocyte lipid-binding protein FABP4 in complex with fluor... -

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Basic information

Entry
Database: PDB / ID: 6ayl
TitleHuman adipocyte lipid-binding protein FABP4 in complex with fluorescein
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytoplasm / 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
2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsPozharski, E.
CitationJournal: To Be Published
Title: To be published
Authors: Pozharski, E. / St John, F.S.
History
DepositionSep 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,1503
Polymers15,4861
Non-polymers6652
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-2 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.190, 53.010, 74.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein, adipocyte / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / AFABP / Fatty ...Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / AFABP / Fatty acid-binding protein 4


Mass: 15485.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P15090
#2: Chemical ChemComp-FLU / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / FLUORESCEIN


Mass: 332.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H12O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M sodium citrate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.86→75 Å / Num. obs: 11207 / % possible obs: 96.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 32.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.042 / Net I/av σ(I): 9.7 / Net I/σ(I): 13.9
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.204 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 501 / CC1/2: 0.391 / Rpim(I) all: 0.921 / % possible all: 73.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RZY

3rzy


Resolution: 1.86→37.49 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.232 548 4.91 %RANDOM
Rwork0.211 ---
obs0.212 11169 95.9 %-
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--17.4827 Å20 Å20 Å2
2--2.2034 Å20 Å2
3---15.2793 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 1.86→37.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 50 51 1086
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011086HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.11481HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d363SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes22HARMONIC2
X-RAY DIFFRACTIONt_gen_planes225HARMONIC5
X-RAY DIFFRACTIONt_it1086HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion19.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion147SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1224SEMIHARMONIC4
LS refinement shellResolution: 1.86→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 107 4.72 %
Rwork0.237 2161 -
all0.238 2268 -
obs--83.46 %

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