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- PDB-3vg2: Iodide derivative of human LFABP -

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Basic information

Entry
Database: PDB / ID: 3vg2
TitleIodide derivative of human LFABP
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / LFABP / Iodide / Copper Kalpha / Palmitic acid
Function / homology
Function and homology information


response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / 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 / phospholipid binding / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / 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: 2.4 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 20, 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

Downloads & links

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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
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.979, 57.781, 74.862
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.: 64 / 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: 2.15 Å3/Da / Density % sol: 42.7 % / Mosaicity: 0.624 °
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: 2.22→50 Å / Num. obs: 6640 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.103 / Χ2: 1.3 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.22-2.34.90.3926211.248196.6
2.3-2.395.70.366371.196199.5
2.39-2.55.70.3456461.261199.7
2.5-2.635.70.2436661.129199.7
2.63-2.85.70.2166331.2081100
2.8-3.015.70.1576621.1791100
3.01-3.325.80.0976651.1811100
3.32-3.85.70.0686841.2561100
3.8-4.785.70.0576861.5441100
4.78-505.20.0627401.779199.6

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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: 2.4→8 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.837 / WRfactor Rfree: 0.2768 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.7832 / SU B: 10.452 / SU ML: 0.246 / SU R Cruickshank DPI: 1.2837 / SU Rfree: 0.3804 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3122 497 9.7 %RANDOM
Rwork0.2065 ---
obs0.2165 5106 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.01 Å2 / Biso mean: 23.3338 Å2 / Biso min: 9.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2---0.95 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 41 64 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221048
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9881395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60826.74443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07715204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.834152
X-RAY DIFFRACTIONr_chiral_restr0.0870.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02732
X-RAY DIFFRACTIONr_nbd_refined0.220.2438
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.25
X-RAY DIFFRACTIONr_mcbond_it0.5381.5642
X-RAY DIFFRACTIONr_mcangle_it0.93721033
X-RAY DIFFRACTIONr_scbond_it1.6223426
X-RAY DIFFRACTIONr_scangle_it2.6474.5361
LS refinement shellResolution: 2.4→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 34 -
Rwork0.256 294 -
all-328 -
obs--99.39 %

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