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- PDB-3hon: Crystal Structure of Human Collagen XVIII Trimerization Domain (c... -

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Basic information

Entry
Database: PDB / ID: 3hon
TitleCrystal Structure of Human Collagen XVIII Trimerization Domain (cubic form)
ComponentsCollagen alpha-1(XVIII) chain
KeywordsPROTEIN BINDING / collagen triple helix / trimerization domain / collagen XVIII / multiplexin / Alternative promoter usage / Alternative splicing / Cell adhesion / Collagen / Disulfide bond / Extracellular matrix / Glycoprotein / Hydroxylation / Metal-binding / Polymorphism / Secreted / Zinc
Function / homology
Function and homology information


response to hydrostatic pressure / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / notochord development / Collagen biosynthesis and modifying enzymes / Laminin interactions / endothelial cell morphogenesis / collagen trimer / collagen fibril organization / Assembly of collagen fibrils and other multimeric structures ...response to hydrostatic pressure / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / notochord development / Collagen biosynthesis and modifying enzymes / Laminin interactions / endothelial cell morphogenesis / collagen trimer / collagen fibril organization / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation / basement membrane / Integrin cell surface interactions / visual perception / skeletal system development / animal organ morphogenesis / angiogenesis / collagen-containing extracellular matrix / cell adhesion / response to xenobiotic stimulus / negative regulation of cell population proliferation / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
YefM-like fold - #70 / Domain of unknown function DUF959, collagen XVIII, N-terminal / Collagen alpha-1(XVIII) chain, frizzled domain / Collagen type XV/XVIII, trimerization domain / Domain of Unknown Function (DUF959) / Collagen trimerization domain / Collagenase NC10/endostatin / Collagenase NC10 and Endostatin / : / YefM-like fold ...YefM-like fold - #70 / Domain of unknown function DUF959, collagen XVIII, N-terminal / Collagen alpha-1(XVIII) chain, frizzled domain / Collagen type XV/XVIII, trimerization domain / Domain of Unknown Function (DUF959) / Collagen trimerization domain / Collagenase NC10/endostatin / Collagenase NC10 and Endostatin / : / YefM-like fold / Thrombospondin N-terminal -like domains. / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin-like/link domain superfamily / C-type lectin fold / Concanavalin A-like lectin/glucanase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Collagen alpha-1(XVIII) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBoudko, S.P. / Bachinger, H.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of human collagen XVIII trimerization domain: A novel collagen trimerization Fold.
Authors: Boudko, S.P. / Sasaki, T. / Engel, J. / Lerch, T.F. / Nix, J. / Chapman, M.S. / Bachinger, H.P.
History
DepositionJun 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen alpha-1(XVIII) chain


Theoretical massNumber of molelcules
Total (without water)6,4421
Polymers6,4421
Non-polymers00
Water0
1
A: Collagen alpha-1(XVIII) chain

A: Collagen alpha-1(XVIII) chain

A: Collagen alpha-1(XVIII) chain


Theoretical massNumber of molelcules
Total (without water)19,3273
Polymers19,3273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5870 Å2
ΔGint-26 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.876, 94.876, 94.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Collagen alpha-1(XVIII) chain / Endostatin


Mass: 6442.368 Da / Num. of mol.: 1 / Fragment: UNP residues 1441-1496 / Mutation: A1441G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL18A1 / Plasmid: pET23d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39060

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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: 55.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.25M MgCl2, 0.1M BisTris, 18-22% (w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.106 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 24, 2008
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.106 Å / Relative weight: 1
ReflectionResolution: 3→38.8 Å / Num. all: 1634 / Num. obs: 1634 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Biso Wilson estimate: 100.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.077 / Net I/σ(I): 25.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 4 / Num. unique all: 233 / Rsym value: 0.682 / % possible all: 100

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Processing

Software
NameVersionClassification
JBluIce-EPICSGUIdata collection
Blu-IceIcedata collection
PHENIXmodel building
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38.73 Å / Rfactor Rfree error: 0.032 / Data cutoff high absF: 1256071.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.288 80 4.9 %RANDOM
Rwork0.279 ---
obs0.279 1625 99.9 %-
all-1627 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 90.6924 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 93.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.84 Å
Refinement stepCycle: LAST / Resolution: 3→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms443 0 0 0 443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.942
X-RAY DIFFRACTIONc_scbond_it1.472
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.097 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 20 7.6 %
Rwork0.437 244 -
obs--100 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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