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- PDB-3sao: The Siderocalin Ex-FABP functions through dual ligand specificities -

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Basic information

Entry
Database: PDB / ID: 3sao
TitleThe Siderocalin Ex-FABP functions through dual ligand specificities
ComponentsExtracellular fatty acid-binding protein
KeywordsTRANSPORT PROTEIN / Beta-Barrel / Siderophore Binding Protein
Function / homology
Function and homology information


cellular response to linoleic acid / muscle cell development => GO:0055001 / stearic acid binding / response to linoleic acid / chondrocyte hypertrophy / cellular lipid metabolic process / linoleic acid binding / response to xenobiotic stimulus => GO:0009410 / positive regulation of chondrocyte differentiation / oleic acid binding ...cellular response to linoleic acid / muscle cell development => GO:0055001 / stearic acid binding / response to linoleic acid / chondrocyte hypertrophy / cellular lipid metabolic process / linoleic acid binding / response to xenobiotic stimulus => GO:0009410 / positive regulation of chondrocyte differentiation / oleic acid binding / embryo development ending in birth or egg hatching / arachidonic acid binding / response to corticosterone / positive regulation of myotube differentiation / fatty acid transport / positive regulation of myoblast differentiation / fatty acid homeostasis / chondrocyte differentiation / long-chain fatty acid transport / response to cytokine / acute-phase response / fatty acid binding / response to toxic substance / heart development / cell population proliferation / response to lipopolysaccharide / cell differentiation / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-BENZOIC ACID / : / Chem-NKN / Extracellular fatty acid-binding protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCorrenti, C. / Strong, R.K. / Clifton, M.C.
CitationJournal: Structure / Year: 2011
Title: Galline Ex-FABP Is an Antibacterial Siderocalin and a Lysophosphatidic Acid Sensor Functioning through Dual Ligand Specificities.
Authors: Correnti, C. / Clifton, M.C. / Abergel, R.J. / Allred, B. / Hoette, T.M. / Ruiz, M. / Cancedda, R. / Raymond, K.N. / Descalzi, F. / Strong, R.K.
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Remark 999Author state that R26A E149A E150A are point mutants they introduced while V74L is a conserved ...Author state that R26A E149A E150A are point mutants they introduced while V74L is a conserved mutation in the gene they worked with.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular fatty acid-binding protein
B: Extracellular fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4647
Polymers36,3982
Non-polymers1,0675
Water2,414134
1
A: Extracellular fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5812
Polymers18,1991
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracellular fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8835
Polymers18,1991
Non-polymers6844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.950, 68.890, 117.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Extracellular fatty acid-binding protein / Ex-FABP / Protein Ch21 / Quiescence-specific protein / p20K


Mass: 18198.789 Da / Num. of mol.: 2 / Fragment: residues 23-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: EXFABP / Production host: Escherichia coli (E. coli) / References: UniProt: P21760

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Non-polymers , 5 types, 139 molecules

#2: Chemical ChemComp-NKN / (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate / 14:0 LPA / myristoyl lysophosphatidic acid


Mass: 382.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H35O7P
#3: Chemical ChemComp-DBH / 2,3-DIHYDROXY-BENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 4000, 0.1M Tris, 0.2M sodium acetate, 10% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2010
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→44.68 Å / Num. obs: 27696 / % possible obs: 94.2 % / Redundancy: 4.87 % / Rmerge(I) obs: 0.058 / Χ2: 0.94 / Net I/σ(I): 11 / Scaling rejects: 1020
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.8-1.864.860.4173.31343727301.3594.4
1.86-1.944.870.3253.91334327271.1795.5
1.94-2.034.860.2544.61354127751.0895.6
2.03-2.134.880.1965.91360727720.9895.3
2.13-2.274.880.1547.41353027550.8995
2.27-2.444.820.1249.31358027660.8995.2
2.44-2.694.880.09511.91377827940.8294.7
2.69-3.084.950.07514.71374027680.7294.4
3.08-3.884.890.06618.11372727930.7993
3.88-44.684.840.03930.11371028160.7789.1

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.3Ddata reduction
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUP and 1EW3 were superimposed and used as single search model ensemble.

1yup

1ew3


Resolution: 1.8→44.68 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.962 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 1361 4.9 %RANDOM
Rwork0.2022 ---
obs0.2037 27646 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 100.3 Å2 / Biso mean: 51.0918 Å2 / Biso min: 32.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.02 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 50 134 2482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222398
X-RAY DIFFRACTIONr_bond_other_d0.0010.021617
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9773244
X-RAY DIFFRACTIONr_angle_other_deg0.74733925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.8422.592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91615398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0551518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02507
X-RAY DIFFRACTIONr_mcbond_it1.86621496
X-RAY DIFFRACTIONr_mcbond_other0.6112600
X-RAY DIFFRACTIONr_mcangle_it2.97632398
X-RAY DIFFRACTIONr_scbond_it4.3424902
X-RAY DIFFRACTIONr_scangle_it6.0446844
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 106 -
Rwork0.231 1888 -
all-1994 -
obs--94.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1254-0.5649-0.25474.37770.31384.2721-0.1160.2136-0.0477-0.3117-0.0031-0.32880.15180.51070.11910.1630.04460.01860.1970.01210.1138-10.708-2.382-16.732
21.1311-0.9844-0.42892.725-0.80521.4733-0.1579-0.08080.08020.04410.15810.1054-0.07520.0373-0.00020.17590.0509-0.07610.1124-0.02720.15-12.6178.688-11.277
35.41182.71043.49259.24243.46687.346-0.04160.1696-0.1866-0.67130.2575-0.1306-0.5337-0.1292-0.21590.2570.0644-0.01650.0838-0.02510.0915-13.41613.543-22.909
40.8374-1.0115-1.12893.30910.78414.7102-0.06330.03050.0032-0.1136-0.066-0.11740.0677-0.07740.12930.19890.0315-0.03990.1972-0.03390.1401-16.336-1.276-23.794
52.9827-0.4333-1.80793.1760.71425.0393-0.0416-0.22580.21450.27430.06460.07090.3350.2232-0.0230.08780.06090.00240.15430.01950.1975-12.830.31-10.568
62.0716-1.0346-0.20042.9071-1.17613.265-0.0594-0.2635-0.1137-0.04680.04050.08180.0214-0.03960.0190.1157-0.0302-0.02830.1786-0.02760.1648-28.781-2.311-46.622
72.3207-0.71030.02044.7473-2.30824.3690.0650.06170.0099-0.2069-0.0604-0.0008-0.0263-0.0895-0.00470.1364-0.0068-0.01530.1659-0.01280.1799-29.805-4.311-54.646
81.5268-0.11650.82611.79781.38272.52360.2337-0.03850.1068-0.495-0.2586-0.0194-0.33-0.09240.02480.14010.01060.05620.1194-0.00290.1473-32.1514.759-55.896
93.6367-2.07011.51731.499-0.47391.8661-0.0447-0.27730.17670.01760.0172-0.0401-0.0833-0.18680.02740.1172-0.0308-0.01410.1943-0.01610.194-27.9923.534-45.834
104.0946-1.83051.57735.31992.24743.5364-0.034-0.51220.11390.25480.2629-0.33270.3852-0.1436-0.2290.1272-0.03030.03560.21390.06260.1649-28.165-5.738-41.829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 37
2X-RAY DIFFRACTION2A38 - 64
3X-RAY DIFFRACTION3A65 - 85
4X-RAY DIFFRACTION4A86 - 137
5X-RAY DIFFRACTION5A138 - 160
6X-RAY DIFFRACTION6B6 - 28
7X-RAY DIFFRACTION7B29 - 57
8X-RAY DIFFRACTION8B58 - 76
9X-RAY DIFFRACTION9B77 - 135
10X-RAY DIFFRACTION10B136 - 154

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