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- PDB-3b2k: Iodide derivative of human LFABP -

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Basic information

Entry
Database: PDB / ID: 3b2k
TitleIodide derivative of human LFABP
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / LFABP / Ioide / Copper Kalpha / Palmitic acid
Function / homology
Function and homology information


cellular detoxification / Heme degradation / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / PPARA activates gene expression / Cytoprotection by HMOX1 ...cellular detoxification / Heme degradation / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / PPARA activates gene expression / Cytoprotection by HMOX1 / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / PALMITIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo Sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsSharma, A. / Yogavel, M. / Sharma, A.
CitationJournal: J.Struct.Funct.Genom. / Year: 2012
Title: Utility of anion and cation combinations for phasing of protein structures.
Authors: Sharma, A. / Yogavel, M. / Sharma, A.
History
DepositionAug 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Mar 13, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,7478
Polymers14,6001
Non-polymers1,1477
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.352, 57.070, 74.892
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver-type fatty acid-binding protein / L-FABP


Mass: 14599.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo Sapiens (human) / Gene: FABP1, FABPL / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P07148
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.22 Å3/Da / Density % sol: 44.63 % / Mosaicity: 1.018 °
Crystal growTemperature: 293 K / Method: hanging drop / pH: 8
Details: 30% PEG MME 2000, 0.15M KBr, pH 8.0, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 10, 2009 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 13416 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.082 / Χ2: 1.341 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.73-1.796.60.64812281.062186.5
1.79-1.867.30.44212621.111192
1.86-1.957.30.30812811.156192.6
1.95-2.057.30.20913191.229193
2.05-2.187.30.16113171.222194.3
2.18-2.357.30.13413431.224194.8
2.35-2.587.30.10813481.32195.2
2.58-2.967.20.08213741.373196.6
2.96-3.737.10.05114241.69197.4
3.73-506.50.04915201.951197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→8 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2578 / WRfactor Rwork: 0.1985 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8054 / SU B: 3.217 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1687 / SU Rfree: 0.1664 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 1309 9.9 %RANDOM
Rwork0.2086 ---
obs0.215 13213 94.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.17 Å2 / Biso mean: 20.2442 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2---0.82 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.73→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 41 208 1246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221103
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.9891482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7835148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99527.08348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7815220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.142152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02792
X-RAY DIFFRACTIONr_nbd_refined0.1830.2513
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2731
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2177
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.225
X-RAY DIFFRACTIONr_mcbond_it0.4661.5666
X-RAY DIFFRACTIONr_mcangle_it0.82421089
X-RAY DIFFRACTIONr_scbond_it1.1793451
X-RAY DIFFRACTIONr_scangle_it1.9764.5384
LS refinement shellResolution: 1.73→1.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.578 87 -
Rwork0.361 774 -
all-861 -
obs--87.23 %

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