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- PDB-3n3f: Crystal Structure of the Human Collagen XV Trimerization Domain: ... -

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Basic information

Entry
Database: PDB / ID: 3n3f
TitleCrystal Structure of the Human Collagen XV Trimerization Domain: A Potent Trimerizing Unit Common to Multiplexin Collagens
ComponentsCollagen alpha-1(XV) chain
KeywordsPROTEIN BINDING / collagen / extracellular matrix / basement membrane / collagen XV / trimerization domain / folding / association / chain selection / triple helix / multiplexin / collagen XVIII
Function / homology
Function and homology information


collagen type XV trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / basement membrane / : / angiogenesis / cell differentiation ...collagen type XV trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / basement membrane / : / angiogenesis / cell differentiation / cell adhesion / endoplasmic reticulum lumen / endoplasmic reticulum / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
YefM-like fold - #70 / Collagenase NC10/endostatin / Collagen type XV/XVIII, trimerization domain / Collagenase NC10 and Endostatin / Collagen trimerization domain / : / Thrombospondin N-terminal -like domains. / YefM-like fold / Concanavalin A-like lectin/glucanases superfamily / : ...YefM-like fold - #70 / Collagenase NC10/endostatin / Collagen type XV/XVIII, trimerization domain / Collagenase NC10 and Endostatin / Collagen trimerization domain / : / Thrombospondin N-terminal -like domains. / YefM-like fold / Concanavalin A-like lectin/glucanases superfamily / : / 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(XV) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.005 Å
AuthorsWirz, J.A.
CitationJournal: Matrix Biol. / Year: 2011
Title: Crystal structure of the human collagen XV trimerization domain: A potent trimerizing unit common to multiplexin collagens.
Authors: Wirz, J.A. / Boudko, S.P. / Lerch, T.F. / Chapman, M.S. / Bachinger, H.P.
History
DepositionMay 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen alpha-1(XV) chain
B: Collagen alpha-1(XV) chain


Theoretical massNumber of molelcules
Total (without water)12,5192
Polymers12,5192
Non-polymers00
Water57632
1
A: Collagen alpha-1(XV) chain

A: Collagen alpha-1(XV) chain

A: Collagen alpha-1(XV) chain


Theoretical massNumber of molelcules
Total (without water)18,7783
Polymers18,7783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4740 Å2
ΔGint-38 kcal/mol
Surface area8630 Å2
MethodPISA
2
B: Collagen alpha-1(XV) chain

B: Collagen alpha-1(XV) chain

B: Collagen alpha-1(XV) chain


Theoretical massNumber of molelcules
Total (without water)18,7783
Polymers18,7783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4510 Å2
ΔGint-41 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.120, 49.120, 65.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Collagen alpha-1(XV) chain / Endostatin / Endostatin-XV / Restin / Related to endostatin


Mass: 6259.278 Da / Num. of mol.: 2 / Fragment: UNP residues 1133-1186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL15A1 / Plasmid: pET23-HisTag-Trx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39059
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.82 Å3/Da / Density % sol: 32.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris, 0.2 M MgCl2, 30% (w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 19, 2009
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.005→42.539 Å / Num. all: 6095 / Num. obs: 6095 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 22.838 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 35.4
Reflection shellResolution: 2.005→2.01 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 15.6 / Num. unique all: 881 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.49 / Cor.coef. Fo:Fc: 0.48
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3HSH

3hsh


Resolution: 2.005→35.69 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 343 5.6 %RANDOM
Rwork0.216 ---
all-6126 --
obs-6079 99.2 %-
Solvent computationBsol: 52.109 Å2
Displacement parametersBiso max: 65.98 Å2 / Biso mean: 26.816 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.168 Å20 Å20 Å2
2--0.168 Å20 Å2
3----0.337 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.005→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms874 0 0 32 906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.097
LS refinement shellResolution: 2.005→2.07 Å
RfactorNum. reflection% reflection
Rfree0.2075 34 -
Rwork0.2339 --
obs-522 87 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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