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- PDB-3b2h: Iodide derivative of human LFABP at high resolution -

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Basic information

Entry
Database: PDB / ID: 3b2h
TitleIodide derivative of human LFABP at high resolution
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / LFABP / Barium-SAD / 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 / SAD / Resolution: 1.55 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)16,63515
Polymers14,6001
Non-polymers2,03614
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.278, 57.104, 74.723
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.: 12 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.21 Å3/Da / Density % sol: 44.4 % / Mosaicity: 1.062 °
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: 1.55→50 Å / Num. all: 19499 / Num. obs: 19340 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.8 % / Rmerge(I) obs: 0.064 / Χ2: 1.742 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.6112.20.50818591.232197
1.61-1.6712.80.37319061.248199.4
1.67-1.7512.90.27818921.294198.9
1.75-1.8412.90.19319061.452199
1.84-1.9512.80.12619101.578199.5
1.95-2.112.90.09119331.821199.8
2.1-2.3213.10.07719612.1741100
2.32-2.6513.50.06719392.4261100
2.65-3.3413.30.05320102.2061100
3.34-5011.90.05121041.833199.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2434 / WRfactor Rwork: 0.2143 / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8303 / SU B: 1.895 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1197 / SU Rfree: 0.1122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1961 10.2 %RANDOM
Rwork0.2167 ---
all0.2196 19499 --
obs-19340 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.81 Å2 / Biso mean: 21.8202 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.55→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 48 219 1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221157
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.9951561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63527.08348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34915243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.435152
X-RAY DIFFRACTIONr_chiral_restr0.070.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02828
X-RAY DIFFRACTIONr_nbd_refined0.1760.2565
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2776
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2187
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0640.234
X-RAY DIFFRACTIONr_mcbond_it0.4291.5695
X-RAY DIFFRACTIONr_mcangle_it0.80721144
X-RAY DIFFRACTIONr_scbond_it1.1243477
X-RAY DIFFRACTIONr_scangle_it1.9464.5402
LS refinement shellResolution: 1.55→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 128 -
Rwork0.378 1196 -
all-1324 -
obs--96.64 %

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