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- PDB-1a18: PHENANTHROLINE MODIFIED MURINE ADIPOCYTE LIPID BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1a18
TitlePHENANTHROLINE 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 / fatty acid transport / brown fat cell differentiation / cholesterol homeostasis ...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 / fatty acid transport / brown fat cell differentiation / 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 protein family / Lipocalin/cytosolic fatty-acid binding 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 23, 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 2.0Aug 2, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADIPOCYTE LIPID BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,7751
Polymers14,7751
Non-polymers00
Water68538
1
A: ADIPOCYTE LIPID BINDING PROTEIN

A: ADIPOCYTE LIPID BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,5502
Polymers29,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_553x,-y,-z-21
Unit cell
Length a, b, c (Å)80.020, 97.150, 49.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1023-

HOH

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Components

#1: Protein ADIPOCYTE LIPID BINDING PROTEIN / ALBP-PHEN


Mass: 14774.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROTEIN MODIFIED BY REACTION WITH IODOACETAMIDO-1,10-PHENANTHROLINE
Source: (gene. exp.) Mus musculus (house mouse)
Description: SEE DAVIES AND DISTEFANO, JACS 119, 11643- 11652 (1977)
Cell: ADIPOCYTE / Production host: Escherichia coli (E. coli) / References: UniProt: P04117
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.2 Å3/Da / Density % sol: 45.6 %
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-ID
110 mg/mlprotein1drop
220 mMHEPES1drop
328-31 %PEG80001reservoir
40.1-0.25 Mammonium sulfate1reservoir
50.1 Msodium cacodylate1reservoir

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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
Num. measured all: 34268 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Rmerge(I) obs: 0.325

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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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.487

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