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- PDB-8r5w: Crystal structure of the three anaphylatoxin-like modules in fibulin-2 -

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Basic information

Entry
Database: PDB / ID: 8r5w
TitleCrystal structure of the three anaphylatoxin-like modules in fibulin-2
ComponentsFibulin-2
KeywordsSTRUCTURAL PROTEIN / Extracellular matrix / Fibulins / anaphylatoxin-like
Function / homology
Function and homology information


Molecules associated with elastic fibres / extracellular matrix binding / positive regulation of cell-substrate adhesion / collagen-containing extracellular matrix / calcium ion binding / extracellular region
Similarity search - Function
Complement Clr-like EGF domain / Complement Clr-like EGF-like / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / : / Calcium-binding EGF domain / Coagulation Factor Xa inhibitory site ...Complement Clr-like EGF domain / Complement Clr-like EGF-like / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / : / Calcium-binding EGF domain / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSohail, A.A. / Koski, M.K. / Ruddock, L.W.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland272573 Finland
CitationJournal: Sci Rep / Year: 2024
Title: Biophysical and structural studies of fibulin-2
Authors: Sohail, A.A. / Koski, M.K. / Ruddock, L.W.
History
DepositionNov 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibulin-2
B: Fibulin-2
C: Fibulin-2
D: Fibulin-2
E: Fibulin-2
F: Fibulin-2
G: Fibulin-2
H: Fibulin-2


Theoretical massNumber of molelcules
Total (without water)110,6618
Polymers110,6618
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Static light scattering was done to show that the molecule forms a dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.680, 34.510, 106.890
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fibulin-2


Mass: 13832.585 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fbln2 / Production host: Escherichia coli B (bacteria) / References: UniProt: P37889
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.72 Å3/Da / Density % sol: 28.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M potassium nitrate, 2 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.97→48.8 Å / Num. obs: 54442 / % possible obs: 99.87 % / Redundancy: 6.8 % / CC1/2: 0.9993 / Net I/σ(I): 8.4
Reflection shellResolution: 1.97→2 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2700 / CC1/2: 0.329 / % possible all: 99.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.8 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 20.487 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29742 1998 5.1 %RANDOM
Rwork0.24279 ---
obs0.24544 37274 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.605 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20.47 Å2
2--0.9 Å2-0 Å2
3----3.72 Å2
Refinement stepCycle: 1 / Resolution: 2.2→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 0 108 6557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126624
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165966
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.8178921
X-RAY DIFFRACTIONr_angle_other_deg0.5291.7813869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.135861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.217535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.696101187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021386
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1434.0033474
X-RAY DIFFRACTIONr_mcbond_other4.1434.0033474
X-RAY DIFFRACTIONr_mcangle_it6.1147.1414304
X-RAY DIFFRACTIONr_mcangle_other6.1147.1434305
X-RAY DIFFRACTIONr_scbond_it5.1664.7283150
X-RAY DIFFRACTIONr_scbond_other5.1624.7273149
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0268.4434611
X-RAY DIFFRACTIONr_long_range_B_refined10.69250.587452
X-RAY DIFFRACTIONr_long_range_B_other10.69550.497443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 120 -
Rwork0.329 2740 -
obs--100 %
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)
11.8222-0.56481.17650.8234-0.49931.5614-0.0227-0.06580.04870.03710.0250.0993-0.0902-0.1186-0.00230.1028-0.02160.01090.08350.01080.172840.22230.526718.9084
22.3118-1.10621.26451.1515-1.12013.13220.00010.01190.0591-0.07910.06540.0122-0.0531-0.0308-0.06550.0611-0.0162-0.01670.0716-0.02810.09549.66371.54169.4122
32.23411.45131.23892.42921.86893.02670.04890.00020.0176-0.0249-0.0025-0.0893-0.08810.005-0.04640.01030.01040.01660.10990.01230.065175.673416.684944.3645
41.43531.10960.96191.76621.35412.0917-0.01050.035-0.07-0.12510.0275-0.201-0.07360.0062-0.0170.08590.03440.0630.13240.01010.210486.278616.16936.1116
51.5512-0.56221.21770.7599-0.79471.5886-0.0763-0.07820.00150.06170.08030.053-0.1278-0.1494-0.00410.1417-0.01820.03390.1653-0.04930.170562.10120.114272.9264
62.3746-0.81720.88351.5139-1.07562.3377-0.01660.01270.0978-0.01390.0234-0.1058-0.05470.0282-0.00680.0429-0.0226-0.00040.1254-0.07550.062471.37550.403363.0876
72.31751.01230.95231.69881.51663.02110.00240.0609-0.0099-0.03650.0478-0.0122-0.1302-0.0206-0.05020.01540.0177-0.00010.04760.03720.09198.333616.043797.3747
81.54410.83590.3691.64671.08392.334-0.08770.0230.0334-0.05840.0322-0.0011-0.0220.23850.05540.09370.03720.04470.11580.00930.1582108.99216.342188.9117
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A419 - 545
2X-RAY DIFFRACTION2B427 - 545
3X-RAY DIFFRACTION3C427 - 545
4X-RAY DIFFRACTION4D423 - 544
5X-RAY DIFFRACTION5E419 - 544
6X-RAY DIFFRACTION6F427 - 545
7X-RAY DIFFRACTION7G427 - 545
8X-RAY DIFFRACTION8H426 - 544

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