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- PDB-1uzj: Integrin binding cbEGF22-TB4-cbEGF33 fragment of human fibrillin-... -

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Basic information

Entry
Database: PDB / ID: 1uzj
TitleIntegrin binding cbEGF22-TB4-cbEGF33 fragment of human fibrillin-1, holo form.
ComponentsFIBRILLIN-1
KeywordsMATRIX PROTEIN / EXTRA-CELLULAR MATRIX / FIBRILLIN-1 / CBEGF DOMAIN / TB DOMAIN MATRIX PROTEIN
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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsLee, S.S.J. / Knott, V. / Harlos, K. / Handford, P.A. / Stuart, D.I.
CitationJournal: Structure / Year: 2004
Title: Structure of the Integrin Binding Fragment from Fibrillin-1 Gives New Insights Into Microfibril Organization
Authors: Lee, S.S.J. / Knott, V. / Jovanovi, J. / Harlos, K. / Grimes, J. / Choulier, L. / Mardon, H. / Stuart, D.I. / Handford, P.A.
History
DepositionMar 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBRILLIN-1
B: FIBRILLIN-1
C: FIBRILLIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2389
Polymers51,9973
Non-polymers2406
Water3,873215
1
A: FIBRILLIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4133
Polymers17,3321
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FIBRILLIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4133
Polymers17,3321
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: FIBRILLIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4133
Polymers17,3321
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.100, 105.600, 65.000
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FIBRILLIN-1


Mass: 17332.436 Da / Num. of mol.: 3 / Fragment: BEGF22-TB4-CBEGF23, RESIDUES 1486-1647
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EXTRA-ELLULAR MATRIX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P35555
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growpH: 8.5
Details: 5MG/ML PROTEIN IN 10MM MES 10MM CACL2 PH6. DEHYDRATED AGAINST: 15% PEG 8000, 10MM MES PH 6 10MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2000 / Details: MIRRORS/MONOCHROMATOR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 25753 / % possible obs: 96.2 % / Redundancy: 2.78 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.7
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 92.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: PBD FIBRILLIN I222 FORM

Resolution: 2.25→30 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1240 4.6 %RANDOM
Rwork0.247 ---
obs0.247 25736 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-2.9 Å2
2--7.7 Å20 Å2
3----8.8 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 6 215 3806
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.54
X-RAY DIFFRACTIONc_mcangle_it4.85
X-RAY DIFFRACTIONc_scbond_it5.15
X-RAY DIFFRACTIONc_scangle_it6.28
LS refinement shellResolution: 2.25→2.28 Å / Total num. of bins used: 24 /
RfactorNum. reflection
Rfree0.329 40
Rwork0.288 969

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