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- PDB-5n86: Crystal structure of FAS1 domain of hyaluronic acid receptor stab... -

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Basic information

Entry
Database: PDB / ID: 5n86
TitleCrystal structure of FAS1 domain of hyaluronic acid receptor stabilin-2
ComponentsStabilin-2
KeywordsCELL ADHESION / FAS1 domain / hyaluronic acid receptor / stabilin-2 / Stab2
Function / homology
Function and homology information


Scavenging by Class H Receptors / Hyaluronan uptake and degradation / hyaluronic acid binding / low-density lipoprotein particle receptor activity / hyaluronan catabolic process / low-density lipoprotein particle binding / scavenger receptor activity / plasma membrane => GO:0005886 / protein-disulfide reductase activity / receptor-mediated endocytosis ...Scavenging by Class H Receptors / Hyaluronan uptake and degradation / hyaluronic acid binding / low-density lipoprotein particle receptor activity / hyaluronan catabolic process / low-density lipoprotein particle binding / scavenger receptor activity / plasma membrane => GO:0005886 / protein-disulfide reductase activity / receptor-mediated endocytosis / endocytosis / endocytic vesicle membrane / angiogenesis / cell adhesion / defense response to Gram-positive bacterium / defense response to bacterium / external side of plasma membrane / calcium ion binding / plasma membrane / cytosol
Similarity search - Function
FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / EGF domain / EGF domain / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Link domain ...FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / EGF domain / EGF domain / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Link domain / Extracellular link domain / Link domain signature. / Link domain profile. / Link (Hyaluronan-binding) / Laminin-type EGF domain / C-type lectin-like/link domain superfamily / C-type lectin fold / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.484 Å
AuthorsTwarda-Clapa, A. / Labuzek, B. / Grudnik, P. / Dubin, G. / Holak, T.A.
Funding support Poland, 2items
OrganizationGrant numberCountry
National Science CentreUMO-2015/17/N/NZ1/00025 Poland
National Science CentreUMO-2012/06/A/ST5/00224 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystal structure of the FAS1 domain of the hyaluronic acid receptor stabilin-2.
Authors: Twarda-Clapa, A. / Labuzek, B. / Krzemien, D. / Musielak, B. / Grudnik, P. / Dubin, G. / Holak, T.A.
History
DepositionFeb 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stabilin-2
B: Stabilin-2


Theoretical massNumber of molelcules
Total (without water)31,4512
Polymers31,4512
Non-polymers00
Water6,503361
1
A: Stabilin-2


Theoretical massNumber of molelcules
Total (without water)15,7261
Polymers15,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Stabilin-2


Theoretical massNumber of molelcules
Total (without water)15,7261
Polymers15,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.740, 55.830, 87.520
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 Stabilin-2 / FAS1 EGF-like and X-link domain-containing adhesion molecule 2 / Fasciclin / EGF-like / laminin- ...FAS1 EGF-like and X-link domain-containing adhesion molecule 2 / Fasciclin / EGF-like / laminin-type EGF-like and link domain-containing scavenger receptor 2 / FEEL-2 / Hyaluronan receptor for endocytosis


Mass: 15725.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAB2, FEEL2, FELL, FEX2, HARE / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWQ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.8 M sodium/potassium tartrate, 0.5% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.484→47.069 Å / Num. obs: 40147 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 12.52 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.094 / Rsym value: 0.085 / Net I/av σ(I): 4.7 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.484-1.565.90.1833.20.0820.2010.183100
1.56-1.665.60.1434.90.0660.1580.14399.8
1.66-1.775.70.1285.20.0570.140.12899.5
1.77-1.925.80.1165.20.0520.1280.11699.9
1.92-2.15.30.1093.80.0510.1210.10999.7
2.1-2.355.90.0946.30.0420.1030.094100
2.35-2.715.50.0867.40.0390.0950.08699.4
2.71-3.326.10.0798.30.0340.0870.079100
3.32-4.695.40.0738.70.0340.0810.07399.7
4.69-48.745.40.0687.90.0310.0750.06899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata processing
SCALA3.3.21data scaling
PHENIX1.11.1_2575refinement
MOLREPphasing
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O70

1o70


Resolution: 1.484→47.069 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.63
RfactorNum. reflection% reflection
Rfree0.1717 2010 5.02 %
Rwork0.1451 --
obs0.1464 40073 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.1 Å2 / Biso mean: 19.0661 Å2 / Biso min: 3.36 Å2
Refinement stepCycle: final / Resolution: 1.484→47.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 0 361 2506
Biso mean---29.8 -
Num. residues----279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082256
X-RAY DIFFRACTIONf_angle_d1.0133080
X-RAY DIFFRACTIONf_chiral_restr0.071361
X-RAY DIFFRACTIONf_plane_restr0.007404
X-RAY DIFFRACTIONf_dihedral_angle_d14.792820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4836-1.52070.2131280.169326692797100
1.5207-1.56180.19561410.161326842825100
1.5618-1.60780.18151450.150626632808100
1.6078-1.65970.18871370.152426892826100
1.6597-1.7190.18771470.15272674282199
1.719-1.78780.1771470.148226942841100
1.7878-1.86920.1881380.151327132851100
1.8692-1.96780.20141420.151826942836100
1.9678-2.0910.16841610.14832679284099
2.091-2.25250.15461320.132327502882100
2.2525-2.47920.16741450.132827152860100
2.4792-2.83780.17031260.13932765289199
2.8378-3.57520.16351530.137927762929100
3.5752-47.09230.16161680.150228983066100
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)
10.8044-1.1453-0.72885.9381-2.21573.18940.07870.0620.1849-0.2674-0.08-0.3439-0.17710.2642-0.05390.1162-0.01820.03220.12380.00860.109616.86434.14632.7503
20.796-0.1317-0.12461.4528-0.32630.91040.04450.21610.0252-0.2490.08150.0614-0.1181-0.138-0.09440.1740.01620.00170.15860.01320.10086.68033.7512-3.4452
31.1971-0.2988-0.38050.7804-0.5261.83140.05850.11950.0861-0.20060.01070.0615-0.05-0.1545-0.05230.1010.0115-0.00410.11230.00590.09016.78052.10884.2661
41.5292-0.1091.34761.06190.54662.6606-0.0812-0.00320.3126-0.22660.01930.0292-0.5571-0.2130.09280.14430.04040.01150.15040.01260.14423.26769.56887.38
50.2316-0.2635-0.010.3412-0.00670.008-0.2399-0.142-0.00650.10570.0051-0.0740.2332-0.46950.10970.2175-0.05610.05170.2664-0.05750.14316.005710.536422.4515
60.78630.1430.7041.4244-0.67863.47710.2256-0.18430.2547-0.0148-0.06620.241-0.4889-0.1999-0.1590.14550.05830.03720.2328-0.03280.168-1.36529.482614.4469
71.2484-0.50680.96580.4897-0.38690.7385-0.2862-0.42540.1820.6029-0.1843-0.6915-0.2836-0.10040.36730.3005-0.0321-0.11610.32390.03540.30647.07821.401227.7868
80.5915-0.31350.19850.76490.12621.40860.1022-0.1210.10660.0887-0.0546-0.0107-0.14110.0095-0.03850.0766-0.0098-0.00080.0995-0.00840.097710.24314.203613.2325
93.8007-2.60650.56833.60190.20480.9198-0.0099-0.0183-0.2446-0.11810.15780.51210.0718-0.4467-0.11120.08130.0027-0.01480.18990.0170.161-2.5914-0.34979.3504
101.4984-0.0939-0.05541.5049-0.44240.7597-0.016-0.1045-0.07030.09370.03080.15010.0543-0.14590.01280.0767-0.00750.00140.09060.00990.095112.3508-17.061521.594
110.41810.03090.47510.00730.1051.76380.09020.2127-0.509-0.1846-0.00760.23330.97110.12860.03890.3664-0.0073-0.00080.1627-0.0320.261317.5414-29.162611.1112
120.98540.2319-0.13510.7594-1.24762.42740.0153-0.23620.01680.5439-0.0946-0.1503-0.26450.12740.02720.12020.002-0.01470.1052-0.00520.082222.7403-14.142622.5851
131.3513-0.0080.35972.3019-0.59341.7951-0.031-0.05050.00810.0354-0.0008-0.1674-0.11150.1006-0.01590.073-0.0065-0.00310.08560.00280.104930.406-11.224617.1704
141.2221-0.2336-0.23880.96490.50051.13110.05640.0775-0.0197-0.16250.0084-0.11550.01840.0426-0.06790.08580.00740.00610.0510.00390.07424.8022-14.04859.467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )A1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 38 )A12 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 62 )A39 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 77 )A63 - 77
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 85 )A78 - 85
6X-RAY DIFFRACTION6chain 'A' and (resid 86 through 100 )A86 - 100
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 112 )A101 - 112
8X-RAY DIFFRACTION8chain 'A' and (resid 113 through 132 )A113 - 132
9X-RAY DIFFRACTION9chain 'A' and (resid 133 through 139 )A133 - 139
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 50 )C0 - 50
11X-RAY DIFFRACTION11chain 'C' and (resid 51 through 62 )C51 - 62
12X-RAY DIFFRACTION12chain 'C' and (resid 63 through 77 )C63 - 77
13X-RAY DIFFRACTION13chain 'C' and (resid 78 through 101 )C78 - 101
14X-RAY DIFFRACTION14chain 'C' and (resid 102 through 139 )C102 - 139

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