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- PDB-2ans: ADIPOCYTE LIPID BINDING PROTEIN COMPLEXED WITH 1-ANILINO-8-NAPHTH... -

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Basic information

Entry
Database: PDB / ID: 2ans
TitleADIPOCYTE LIPID BINDING PROTEIN COMPLEXED WITH 1-ANILINO-8-NAPHTHALENE SULFONATE
ComponentsADIPOCYTE LIPID-BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / FLUORESCENT PROBE
Function / homology
Function and homology information


Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / cholesterol homeostasis ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / cholesterol homeostasis / fatty acid metabolic process / fatty acid binding / response to bacterium / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / nucleoplasm / nucleus / cytosol / cytoplasm
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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
8-ANILINO-1-NAPHTHALENE SULFONATE / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOry, J.J. / Banaszak, L.J.
CitationJournal: Biophys.J. / Year: 1999
Title: Studies of the ligand binding reaction of adipocyte lipid binding protein using the fluorescent probe 1, 8-anilinonaphthalene-8-sulfonate.
Authors: Ory, J.J. / Banaszak, L.J.
History
DepositionJan 19, 1999Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Structure summary
Category: software / struct_keywords / Item: _software.name / _struct_keywords.text
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADIPOCYTE LIPID-BINDING PROTEIN
B: ADIPOCYTE LIPID-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7145
Polymers29,0792
Non-polymers6343
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.800, 96.100, 49.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99105, 0.13205, 0.019552), (0.131421, 0.990854, -0.030598), (-0.023414, -0.027754, -0.999341)
Vector: 33.59208, -1.46339, 26.21906)

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Components

#1: Protein ADIPOCYTE LIPID-BINDING PROTEIN / ALBP / AP2 / A-FABP


Mass: 14539.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P04117
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE


Mass: 299.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13NO3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.34 Å3/Da / Density % sol: 63 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES1reservoir
22 %(v/v)PEG4001reservoir
32.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→24 Å / Num. obs: 12287 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.102
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 2.5 % / Rsym value: 0.312 / % possible all: 58
Reflection
*PLUS
Num. measured all: 74950 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
% possible obs: 58 % / Num. unique obs: 1263 / Rmerge(I) obs: 0.312

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Processing

Software
NameClassification
X-PLORrefinement
X-PLORmodel building
CNSrefinement
XENGENdata reduction
XENGENdata scaling
CNSphasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LIB

1lib


Resolution: 2.5→24 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -10 %RANDOM
Rwork0.189 ---
obs0.189 12287 95 %-
Refinement stepCycle: LAST / Resolution: 2.5→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 43 78 2155
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2ANS.PARAMANS.TOPPAR
X-RAY DIFFRACTION3PARAM.WATCHL.TOPPAR
X-RAY DIFFRACTION4CHL.PARAMTOPH.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.581

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