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- PDB-1dy2: Murine collagen alpha1(XV), endostatin domain -

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Basic information

Entry
Database: PDB / ID: 1dy2
TitleMurine collagen alpha1(XV), endostatin domain
ComponentsCOLLAGEN ALPHA1(XV) CHAIN
KeywordsANGIOGENESIS INHIBITOR
Function / homology
Function and homology information


Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / collagen trimer / basement membrane / : / cell adhesion / endoplasmic reticulum / extracellular space
Similarity search - Function
Collagenase NC10/endostatin / Collagen type XV/XVIII, trimerization domain / Collagenase NC10 and Endostatin / Collagen trimerization domain / : / Thrombospondin N-terminal -like domains. / Concanavalin A-like lectin/glucanases superfamily / : / Laminin G domain / Laminin G domain ...Collagenase NC10/endostatin / Collagen type XV/XVIII, trimerization domain / Collagenase NC10 and Endostatin / Collagen trimerization domain / : / Thrombospondin N-terminal -like domains. / Concanavalin A-like lectin/glucanases superfamily / : / Laminin G domain / Laminin G domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / C-type lectin fold / Concanavalin A-like lectin/glucanase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Collagen alpha-1(XV) chain
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTisi, D. / Hohenester, E. / Sasaki, T. / Timpl, R.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Endostatin Derived from Collagens Xv and Xviii Differ in Structural and Binding Properties, Tissue Distribution and Anti-Angiogenic Activity
Authors: Sasaki, T. / Larsson, H. / Tisi, D. / Claesson-Welsh, L. / Hohenester, E. / Timpl, R.
#1: Journal: Embo J. / Year: 1998
Title: Crystal Structure of the Angiogenesis Inhibitor Endostatin at 1.5 Angstrom Resolution
Authors: Hohenester, E. / Sasaki, T. / Olsen, B.R. / Timpl, R.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Endostatin: An Endogenous Inhibitor of Angiogenesis and Tumor Growth
Authors: O'Reilly, M.S. / Boehm, T. / Shing, Y. / Fukai, N. / Vasios, G. / Lane, W.S. / Flynn, E. / Birkhead, J.R. / Olsen, B.R. / Folkman, J.
History
DepositionJan 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COLLAGEN ALPHA1(XV) CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1822
Polymers20,0861
Non-polymers961
Water81145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.550, 57.700, 71.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL UNIT IS A MONOMER

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Components

#1: Protein COLLAGEN ALPHA1(XV) CHAIN


Mass: 20085.875 Da / Num. of mol.: 1 / Fragment: ENDOSTATIN DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell (production host): EMBRYONIC KIDNEY CELL / Cell line (production host): EBNA-293 / Production host: HOMO SAPIENS (human) / References: UniProt: O35206
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL APLA

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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

Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.01 MTris-HCl1drop
320-30 %(w/v)PEG80001reservoir
40.3 Mammonium sulfate1reservoir
50.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 9225 / % possible obs: 97.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.152 / % possible all: 97.2
Reflection
*PLUS
Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
X-PLORrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KOE

1koe


Resolution: 2→20 Å / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 -10 %RANDOM
Rwork0.2 ---
obs0.2 9062 91.8 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 5 45 1368
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.31
X-RAY DIFFRACTIONx_mcangle_it3.82
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it5.74
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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