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- PDB-3vg5: Barium derivative of human LFABP -

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Basic information

Entry
Database: PDB / ID: 3vg5
TitleBarium derivative of human LFABP
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / LFABP / Barium-SAD / 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
: / PALMITIC ACID / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo Sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 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 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,3875
Polymers14,6001
Non-polymers7884
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.293, 57.122, 74.110
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-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 43.99 % / Mosaicity: 1.923 °
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→50 Å / Num. obs: 9148 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.086 / Χ2: 1.694 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.0712.10.4468311.359194.2
2.07-2.1513.70.3869161.4011100
2.15-2.2513.70.2958781.4421100
2.25-2.3713.80.2589101.4381100
2.37-2.5213.80.1999221.5211100
2.52-2.7113.90.1548841.4851100
2.71-2.9913.80.119291.6061100
2.99-3.4213.80.079171.8181100
3.42-4.3113.60.0569472.1051100
4.31-5012.30.05410142.682199.7

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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: 2→8 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2381 / WRfactor Rwork: 0.2034 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.817 / SU B: 4.841 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2765 / SU Rfree: 0.2026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 895 10 %RANDOM
Rwork0.2143 ---
all0.2181 9148 --
obs-8924 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.95 Å2 / Biso mean: 27.8288 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2---1 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 38 156 1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221068
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.9921427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4875136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35627.02147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73715208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.812152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02764
X-RAY DIFFRACTIONr_nbd_refined0.1890.2447
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2693
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2141
X-RAY DIFFRACTIONr_metal_ion_refined0.130.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.218
X-RAY DIFFRACTIONr_mcbond_it0.5241.5646
X-RAY DIFFRACTIONr_mcangle_it0.96521050
X-RAY DIFFRACTIONr_scbond_it1.4183423
X-RAY DIFFRACTIONr_scangle_it2.5014.5373
LS refinement shellResolution: 2.004→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 62 -
Rwork0.239 526 -
all-588 -
obs--97.19 %

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