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

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Basic information

Entry
Database: PDB / ID: 1uzq
TitleIntegrin binding cbEGF22-TB4-cbEGF33 fragment of human fibrillin-1, apo form cbEGF23 domain only.
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 / 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 / metanephros development / Elastic fibre formation / 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 / metanephros development / Elastic fibre formation / camera-type eye development / Molecules associated with elastic fibres / extracellular matrix structural constituent / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / 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 / Extracellular Matrix Fibrillin / TGF-beta binding (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 / : / TB domain / Extracellular Matrix Fibrillin / TGF-beta binding (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 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 15, 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 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 1, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBRILLIN-1


Theoretical massNumber of molelcules
Total (without water)17,3321
Polymers17,3321
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.400, 70.800, 102.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein FIBRILLIN-1


Mass: 17332.436 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.22 Å3/Da / Density % sol: 41 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: SITTING DROP VAPOUR DIFFUSION, 3 MICROLITRE OF 25MG/ML PROTEIN, 10MM TRIS PH7.5 + 0.5 MICROLITRES OF 40% V/V POLYPROPYLENE GLYCOL P400 + 2.5 MICROLITRES RESERVOIR SOLUTION (0.2M LISULFATE, 0. ...Details: SITTING DROP VAPOUR DIFFUSION, 3 MICROLITRE OF 25MG/ML PROTEIN, 10MM TRIS PH7.5 + 0.5 MICROLITRES OF 40% V/V POLYPROPYLENE GLYCOL P400 + 2.5 MICROLITRES RESERVOIR SOLUTION (0.2M LISULFATE, 0.1M TRIS PH 8.5, 30% PEG 4000) BOTH PROTEIN AND RESERVOIR SOLUTIONS CONTAINED 5MM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542
DetectorType: MARRESEARCH 300MM / Detector: IMAGE PLATE / Date: Dec 15, 2001 / Details: OSMIC BLUE CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 6275 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 5.8 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD FIBRILLIN SM BOUND FORM

Resolution: 2.4→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.33 685 10.8 %RANDOM
Rwork0.254 ---
obs0.254 6275 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.1 Å20 Å20 Å2
2---28.5 Å20 Å2
3---13.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 0 2 1125
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.75
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_it2.93
X-RAY DIFFRACTIONc_mcangle_it4.34
X-RAY DIFFRACTIONc_scbond_it4.14
X-RAY DIFFRACTIONc_scangle_it5.55
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 13 /
RfactorNum. reflection
Rfree0.451 48
Rwork0.391 424

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