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- PDB-3hsh: Crystal structure of human collagen XVIII trimerization domain (T... -

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Basic information

Entry
Database: PDB / ID: 3hsh
TitleCrystal structure of human collagen XVIII trimerization domain (Tetragonal crystal form)
ComponentsCollagen alpha-1(XVIII) chain
KeywordsPROTEIN BINDING / collagen / extracellular matrix / basement membrane / collagen XVIII / trimerization domain / folding / association / chain selection / endostatin / triple helix / Alternative promoter usage / Cell adhesion / Disulfide bond / Glycoprotein / Hydroxylation / Metal-binding / Secreted
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: 1.8 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 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
B: Collagen alpha-1(XVIII) chain
C: Collagen alpha-1(XVIII) chain
D: Collagen alpha-1(XVIII) chain
E: Collagen alpha-1(XVIII) chain
F: Collagen alpha-1(XVIII) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,73228
Polymers38,6546
Non-polymers2,07822
Water4,972276
1
A: Collagen alpha-1(XVIII) chain
B: Collagen alpha-1(XVIII) chain
C: Collagen alpha-1(XVIII) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,93220
Polymers19,3273
Non-polymers1,60517
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-122.7 kcal/mol
Surface area9230 Å2
MethodPISA
2
D: Collagen alpha-1(XVIII) chain
E: Collagen alpha-1(XVIII) chain
F: Collagen alpha-1(XVIII) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7998
Polymers19,3273
Non-polymers4725
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-63.3 kcal/mol
Surface area8180 Å2
MethodPISA
3
A: Collagen alpha-1(XVIII) chain
B: Collagen alpha-1(XVIII) chain
C: Collagen alpha-1(XVIII) chain
D: Collagen alpha-1(XVIII) chain
E: Collagen alpha-1(XVIII) chain
F: Collagen alpha-1(XVIII) chain
hetero molecules

A: Collagen alpha-1(XVIII) chain
B: Collagen alpha-1(XVIII) chain
C: Collagen alpha-1(XVIII) chain
D: Collagen alpha-1(XVIII) chain
E: Collagen alpha-1(XVIII) chain
F: Collagen alpha-1(XVIII) chain
hetero molecules

A: Collagen alpha-1(XVIII) chain
B: Collagen alpha-1(XVIII) chain
C: Collagen alpha-1(XVIII) chain
D: Collagen alpha-1(XVIII) chain
E: Collagen alpha-1(XVIII) chain
F: Collagen alpha-1(XVIII) chain
hetero molecules

A: Collagen alpha-1(XVIII) chain
B: Collagen alpha-1(XVIII) chain
C: Collagen alpha-1(XVIII) chain
D: Collagen alpha-1(XVIII) chain
E: Collagen alpha-1(XVIII) chain
F: Collagen alpha-1(XVIII) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,927112
Polymers154,61724
Non-polymers8,31188
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area81780 Å2
ΔGint-972 kcal/mol
Surface area46970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.745, 71.745, 134.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-55-

SO4

21B-59-

GOL

31C-70-

HOH

41C-254-

HOH

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Components

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


Mass: 6442.368 Da / Num. of mol.: 6 / 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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 1.65M ammonium sulfate, 0.1M citric acid, pH 3.5, 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: 1.8→49.09 Å / Num. obs: 33455 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.9 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.065 / Net I/σ(I): 24.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 5.5 / Num. unique all: 4788 / Rsym value: 0.464 / % possible all: 100

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
Blu-IceIcedata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.524 Å / SU ML: 0.25 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 3336 9.98 %RANDOM
Rwork0.1747 ---
all0.1823 ---
obs0.1795 33423 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.682 Å2 / ksol: 0.375 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→40.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2706 0 119 276 3101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82580.2641330.19971219X-RAY DIFFRACTION99
1.8258-1.8530.20531310.18781231X-RAY DIFFRACTION100
1.853-1.8820.23221250.17491251X-RAY DIFFRACTION100
1.882-1.91290.25561600.18371200X-RAY DIFFRACTION100
1.9129-1.94580.21751590.18311210X-RAY DIFFRACTION100
1.9458-1.98120.24261260.1751246X-RAY DIFFRACTION100
1.9812-2.01930.23081190.16811227X-RAY DIFFRACTION100
2.0193-2.06050.24011290.17691258X-RAY DIFFRACTION100
2.0605-2.10530.21431280.16181246X-RAY DIFFRACTION100
2.1053-2.15430.21041360.15881227X-RAY DIFFRACTION100
2.1543-2.20820.22811430.16451240X-RAY DIFFRACTION100
2.2082-2.26790.20581320.16151234X-RAY DIFFRACTION100
2.2679-2.33460.23561640.17491223X-RAY DIFFRACTION100
2.3346-2.410.22351500.16491243X-RAY DIFFRACTION100
2.41-2.49610.21741370.17161234X-RAY DIFFRACTION100
2.4961-2.5960.23621530.17971240X-RAY DIFFRACTION100
2.596-2.71410.22341110.18521270X-RAY DIFFRACTION100
2.7141-2.85720.21131250.18141279X-RAY DIFFRACTION100
2.8572-3.03610.24511490.1831252X-RAY DIFFRACTION100
3.0361-3.27050.20991390.16891282X-RAY DIFFRACTION100
3.2705-3.59940.18161370.14781277X-RAY DIFFRACTION100
3.5994-4.11980.22161380.15221298X-RAY DIFFRACTION100
4.1198-5.18880.19231560.14641307X-RAY DIFFRACTION100
5.1888-40.53460.26521560.21611393X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43230.0374-0.23140.69470.0250.55820.0026-0.04-0.01610.0275-0.00980.0050.02510.04420.01470.04610.0034-0.00020.05680.01740.095119.114420.98916.0246
21.0430.26410.26860.7417-0.0844-0.50960.0432-0.6209-0.15320.3354-0.0567-0.07750.0811-0.07950.01240.36560.04510.01960.50080.11430.10419.021321.014750.3322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B or chain C
2X-RAY DIFFRACTION2chain D or chain E or chain F

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