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

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Basic information

Entry
Database: PDB / ID: 1uzk
TitleIntegrin binding cbEGF22-TB4-cbEGF33 fragment of human fibrillin-1, Ca bound to cbEGF23 domain only
ComponentsFIBRILLIN-1
KeywordsGLYCOPROTEIN / EXTRA-CELLULAR MATRIX / CALCIUM / TB DOMAIN / FIBRILLIN-1 / DISEASE MUTATION / EXTRACELLULAR MATRIX / POLYMORPHISM / CBEGF DOMAIN / EGF-LIKE DOMAIN
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 / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / TB domain / TGF-beta binding (TB) domain profile. / 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 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 / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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.M. / Choulier, L. / Mardon, H.J. / Stuart, D.I. / Handford, P.A.
History
DepositionMar 13, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2006Provider: 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 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.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

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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)17,4192
Polymers17,3791
Non-polymers401
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.500, 70.800, 102.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

21A-2002-

HOH

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Components

#1: Protein FIBRILLIN-1


Mass: 17379.330 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-CELLULAR 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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFIBRILLIN-1-CONTAINING MICROFIBRILS PROVIDE LONG-TERM FORCE BEARING STRUCTURAL SUPPORT
Sequence detailsFRAGMENT

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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)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9787
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS/MONOCHROMATOR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 25753 / % possible obs: 98.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.8
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.7 / % possible all: 96.5

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Processing

Software
NameClassification
SHELXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD FIBRILLIN SM BOUND FORM

Resolution: 1.35→30 Å / Num. parameters: 11831 / Num. restraintsaints: 14105 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rfree0.261 1612 5 %
obs0.202 -98.3 %
all-32331 -
Solvent computationSolvent model: MOEWS & KRETSINGER
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 1 151 1275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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