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- PDB-1a2d: PYRIDOXAMINE MODIFIED MURINE ADIPOCYTE LIPID BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1a2d
TitlePYRIDOXAMINE MODIFIED MURINE ADIPOCYTE LIPID BINDING PROTEIN
ComponentsADIPOCYTE LIPID BINDING PROTEIN
KeywordsFATTY ACID BINDING PROTEIN / TRANSPORT / PHOSPHORYLATION
Function / homology
Function and homology information


Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / cholesterol homeostasis / response to bacterium ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / cholesterol homeostasis / 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 / nucleoplasm / nucleus / cytoplasm
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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOry, J. / Mazhary, A. / Kuang, H. / Davies, R. / Distefano, M. / Banaszak, L.
CitationJournal: Protein Eng. / Year: 1998
Title: Structural characterization of two synthetic catalysts based on adipocyte lipid-binding protein.
Authors: Ory, J.J. / Mazhary, A. / Kuang, H. / Davies, R.R. / Distefano, M.D. / Banaszak, L.J.
History
DepositionDec 29, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: ADIPOCYTE LIPID BINDING PROTEIN
B: ADIPOCYTE LIPID BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5154
Polymers29,4442
Non-polymers712
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.080, 96.250, 49.800
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 ADIPOCYTE LIPID BINDING PROTEIN / ALBP-PX


Mass: 14721.933 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PROTEIN MODIFIED BY REACTION WITH 5-(2-PYRIDYLDITHIO)PYRIDOXAMINE
Source: (gene. exp.) Mus musculus (house mouse) / Description: SEE KUANG ET AL., JACS 118\:10702-10706 (1996) / Cell: ADIPOCYTE / Production host: Escherichia coli (E. coli) / References: UniProt: P04117
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.4 Å3/Da / Density % sol: 64.4 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMHEPES1drop
320-30 %PEG4001reservoir
40.1-0.25 M1reservoirLi2SO4
50.1 MTris-HCl1reservoir

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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 / Date: Jun 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 7640 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.078 / Net I/σ(I): 13.1
Reflection shellResolution: 2.37→2.52 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.325 / % possible all: 62.4
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. obs: 8916 / % possible obs: 94 % / Num. measured all: 76938 / Rmerge(I) obs: 0.0946
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.75 Å / % possible obs: 78.05 % / Rmerge(I) obs: 0.3021

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIB

1lib


Resolution: 2.4→25 Å / Rfactor Rfree error: 0.0124 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.273 498 6.4 %RANDOM
Rwork0.196 ---
obs0.196 7615 96.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 0 38 1073
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.424 43 8.6 %
Rwork0.327 651 -
obs--75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PHN.PARAMPHN.TOPPAR
Software
*PLUS
Name: X-PLOR / Version: 3.843C / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.395

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