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- PDB-1lmj: NMR Study of the Fibrillin-1 cbEGF12-13 Pair of Ca2+ Binding Epid... -

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Basic information

Entry
Database: PDB / ID: 1lmj
TitleNMR Study of the Fibrillin-1 cbEGF12-13 Pair of Ca2+ Binding Epidermal Growth Factor-like Domains
Componentsfibrillin 1
KeywordsSTRUCTURAL PROTEIN / EGF / calcium / microfibril / neonatal / Marfan syndrome / connective tissue / extracellular matrix
Function / homology
Function and homology information


post-embryonic eye morphogenesis / extracellular matrix constituent conferring elasticity / sequestering of BMP in extracellular matrix / sequestering of TGFbeta in extracellular matrix / microfibril / embryonic eye morphogenesis / negative regulation of osteoclast development / Elastic fibre formation / metanephros development / camera-type eye development ...post-embryonic eye morphogenesis / extracellular matrix constituent conferring elasticity / sequestering of BMP in extracellular matrix / sequestering of TGFbeta in extracellular matrix / microfibril / embryonic eye morphogenesis / negative regulation of osteoclast development / Elastic fibre formation / metanephros development / camera-type eye development / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / extracellular matrix structural constituent / cell adhesion mediated by integrin / lung alveolus development / negative regulation of osteoclast differentiation / TGF-beta receptor signaling activates SMADs / basement membrane / anatomical structure morphogenesis / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / Degradation of the extracellular matrix / extracellular matrix / skeletal system development / Post-translational protein phosphorylation / hormone activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / heparin binding / heart development / gene expression / collagen-containing extracellular matrix / endoplasmic reticulum lumen / calcium ion binding / protein-containing complex binding / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Fibrillin 1, unique N-terminal domain / : / Fibrillin 1 unique N-terminal domain / Fibrillin, first EGF domain / TB domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / EGF domain / EGF domain ...Fibrillin 1, unique N-terminal domain / : / Fibrillin 1 unique N-terminal domain / Fibrillin, first EGF domain / TB domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / 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 / Coagulation Factor Xa inhibitory site / Laminin / 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 signature 1. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSmallridge, R.S. / Whiteman, P. / Werner, J.M. / Campbell, I.D. / Handford, P.A. / Downing, A.K.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Solution Structure and Dynamics of a Calcium Binding Epidermal Growth Factor-like Domain Pair from the Neonatal Region of Human Fibrillin-1.
Authors: Smallridge, R.S. / Whiteman, P. / Werner, J.M. / Campbell, I.D. / Handford, P.A. / Downing, A.K.
History
DepositionMay 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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_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_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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: fibrillin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5903
Polymers9,5101
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with acceptable covalent geometry
RepresentativeModel #6closest to the average

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Components

#1: Protein fibrillin 1


Mass: 9509.739 Da / Num. of mol.: 1 / Fragment: cbEGF12-13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBN1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): NM554 and BL21 / References: UniProt: P35555
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
1233D 15N-separated NOESY
133HMQC-J
143HSQC (slow HN)

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM CaCl2, 4.55 mM Tris, 3 mM protein90% H2O/10% D2O
220 mM CaCl2, 4.55 mM Tris, 3.6 mM protein99.9% D2O
320 mM CaCl2, 4.55 mM Tris, 3.8 mM 15N-protein90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM CaCl2, 4.55 mM Tris / pH: 6.5 / Pressure: ambient / Temperature: 306 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA5001
GE OMEGAGEOMEGA6002
GE OMEGAGEOMEGA7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.81Brungerstructure solution
X-PLOR3.81Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1892 distance constraints including 411 ambiguous constraints, 26 torsion angle phi restraints, 24 restraints for 12 hydrogen bonds RMSD from experimental restraints All 0.013+/-0.001 (1932) ...Details: 1892 distance constraints including 411 ambiguous constraints, 26 torsion angle phi restraints, 24 restraints for 12 hydrogen bonds RMSD from experimental restraints All 0.013+/-0.001 (1932) Intraresidue 0.009+/-0.002 (504) Sequential 0.011+/-0.002 (388) Short-range (i-j<=4) (211) 0.015+/-0.003 Long-range 0.013+/-0.002 (378) Ambiguous 0.015+/-0.002 (411) H-bonds 0.014+/-0.004 (24) Calcium 0.012+/-0.005 (16) RMSD Phi rest. 0.177+/-0.093 (26)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 25

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