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- PDB-2w86: Crystal structure of fibrillin-1 domains cbEGF9hyb2cbEGF10, calci... -

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Basic information

Entry
Database: PDB / ID: 2w86
TitleCrystal structure of fibrillin-1 domains cbEGF9hyb2cbEGF10, calcium saturated form
ComponentsFIBRILLIN-1
KeywordsGLYCOPROTEIN / FIBRILLIN / PHOSPHOPROTEIN / EGF-LIKE DOMAIN / DISEASE MUTATION / CRANIOSYNOSTOSIS / EXTRACELLULAR MATRIX / FIBRILLIN CALCIUM CBEGF HYBRID / CALCIUM / SECRETED / POLYMORPHISM
Function / homology
Function and homology information


post-embryonic eye morphogenesis / regulation of plasma lipoprotein particle levels / extracellular matrix constituent conferring elasticity / embryonic eye morphogenesis / elastic fiber assembly / microfibril / response to peptide / endothelial cell differentiation / metanephros development / response to acetylcholine ...post-embryonic eye morphogenesis / regulation of plasma lipoprotein particle levels / extracellular matrix constituent conferring elasticity / embryonic eye morphogenesis / elastic fiber assembly / microfibril / response to peptide / endothelial cell differentiation / metanephros development / response to acetylcholine / negative regulation of osteoclast development / negative regulation of osteoclast differentiation / camera-type eye development / lung alveolus development / non-collagenous component of basement membrane / collagen fibril organization / Elastic fibre formation / Molecules associated with elastic fibres / cell adhesion mediated by integrin / triglyceride homeostasis / response to nitric oxide / cellular response to insulin-like growth factor stimulus / response to ATP / extracellular matrix structural constituent / skin development / basement membrane / TGF-beta receptor signaling activates SMADs / negative regulation of BMP signaling pathway / skeletal system development / cellular response to transforming growth factor beta stimulus / Integrin cell surface interactions / response to mechanical stimulus / Degradation of the extracellular matrix / gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / glucose metabolic process / Post-translational protein phosphorylation / hormone activity / vasodilation / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / intracellular protein localization / heart development / angiogenesis / heparin binding / glucose homeostasis / response to oxidative stress / extracellular matrix / inflammatory response / response to xenobiotic stimulus / immune response / endoplasmic reticulum lumen / calcium ion binding / protein-containing complex binding / extracellular region / identical protein binding
Similarity search - Function
Fibrillin 1, unique N-terminal domain / : / : / Fibrillin 1 unique N-terminal domain / Fibrillin, first EGF domain / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / TB domain / TB domain / TGF-beta binding (TB) domain superfamily ...Fibrillin 1, unique N-terminal domain / : / : / Fibrillin 1 unique N-terminal domain / Fibrillin, first EGF domain / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / TB domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. / EGF domain / EGF domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / Laminin / Laminin / 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 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Fibrillin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJensen, S.A. / Iqbal, S. / Lowe, E.D. / Redfield, C. / Handford, P.A.
CitationJournal: Structure / Year: 2009
Title: Structure and Interdomain Interactions of a Hybrid Domain: A Disulphide-Rich Module of the Fibrillin/Ltbp Superfamily of Matrix Proteins.
Authors: Jensen, S.A. / Iqbal, S. / Lowe, E.D. / Redfield, C. / Handford, P.A.
History
DepositionJan 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: FIBRILLIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9896
Polymers15,5281
Non-polymers4615
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.232, 47.258, 89.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FIBRILLIN-1 / FIBRILLIN1


Mass: 15527.713 Da / Num. of mol.: 1 / Fragment: CBEGF9HYB2CBEGF10, RESIDUES 807-951
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P35555
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE DEPOSITED STRUCTURE CONTAINS ONLY THE CBEGF9HYB2CBEGF10 DOMAINS

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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: 1.99 Å3/Da / Density % sol: 38.2 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM TRIS PH 7.5, 200 MM NAI, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.04
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 13, 2008
RadiationMonochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.7→29.79 Å / Num. obs: 15382 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 14.46 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 7.6 / % possible all: 100

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→41.75 Å / SU ML: 0.23 / σ(F): 0.09 / Phase error: 19.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 673 5.3 %
Rwork0.1851 --
obs0.1872 12682 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.373 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso mean: 25.19 Å2
Baniso -1Baniso -2Baniso -3
1--5.5055 Å2-0 Å2-0 Å2
2---6.6722 Å2-0 Å2
3----6.4337 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 5 148 1219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061089
X-RAY DIFFRACTIONf_angle_d1.0271459
X-RAY DIFFRACTIONf_dihedral_angle_d16.375397
X-RAY DIFFRACTIONf_chiral_restr0.068170
X-RAY DIFFRACTIONf_plane_restr0.005191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.9390.24061310.16632320X-RAY DIFFRACTION97
1.939-2.13410.2141190.16142349X-RAY DIFFRACTION99
2.1341-2.44290.21391240.17052378X-RAY DIFFRACTION99
2.4429-3.07760.22741350.18372422X-RAY DIFFRACTION100
3.0776-41.76080.21781640.20272540X-RAY DIFFRACTION100
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)
10.9758-0.12480.10560.68550.089-0.08430.10220.1967-0.01290.1692-0.1682-0.0931-0.14190.14610.04810.21280.0163-0.03410.19490.00670.156921.971625.537742.1944
20.2547-0.0096-0.2379-0.0373-0.16970.331-0.03030.0325-0.0126-0.05330.00360.0020.0185-0.08850.01360.1378-0.01130.01390.14-0.00270.13519.824329.286959.6935
30.69420.1521-0.32511.42110.7470.71810.0597-0.0239-0.01830.13890.0133-0.01770.10590.2263-0.04470.1501-0.00690.01580.15030.00440.12668.813328.650774.9865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 6:43
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 44:109
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 110:147

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