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- PDB-1koe: ENDOSTATIN -

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Basic information

Entry
Database: PDB / ID: 1koe
TitleENDOSTATIN
ComponentsENDOSTATIN
KeywordsANGIOGENESIS INHIBITOR / COLLAGEN XVIII / NON-COLLAGENEOUS DOMAIN / HEPARIN-BINDING DOMAIN
Function / homology
Function and homology information


vascular endothelial cell proliferation / Activation of Matrix Metalloproteinases / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / blood vessel endothelial cell migration / extracellular matrix structural constituent conferring tensile strength / Integrin cell surface interactions / notochord development ...vascular endothelial cell proliferation / Activation of Matrix Metalloproteinases / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / blood vessel endothelial cell migration / extracellular matrix structural constituent conferring tensile strength / Integrin cell surface interactions / notochord development / endothelial cell morphogenesis / collagen trimer / positive regulation of endothelial cell apoptotic process / endothelial cell apoptotic process / collagen fibril organization / positive regulation of vascular endothelial cell proliferation / basement membrane / positive regulation of blood vessel endothelial cell migration / extracellular matrix organization / skeletal system development / angiogenesis / collagen-containing extracellular matrix / cell adhesion / extracellular space / metal ion binding
Similarity search - Function
Domain of unknown function DUF959, collagen XVIII, N-terminal / Collagen alpha-1(XVIII) chain, frizzled domain / Domain of Unknown Function (DUF959) / 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 ...Domain of unknown function DUF959, collagen XVIII, N-terminal / Collagen alpha-1(XVIII) chain, frizzled domain / Domain of Unknown Function (DUF959) / 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 / Frizzled / : / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / 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(XVIII) chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS, SOLVENT FLATTENING AT 2.2 A RESOLUTION / Resolution: 1.5 Å
AuthorsHohenester, E. / Sasaki, T. / Olsen, B.R. / Timpl, R.
Citation
Journal: EMBO J. / Year: 1998
Title: Crystal structure of the angiogenesis inhibitor endostatin at 1.5 A resolution.
Authors: Hohenester, E. / Sasaki, T. / Olsen, B.R. / Timpl, R.
#1: 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 22, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 31, 2021Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / Item: _entity_src_gen.pdbx_host_org_strain
Revision 1.4Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOSTATIN


Theoretical massNumber of molelcules
Total (without water)18,9501
Polymers18,9501
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.560, 53.950, 65.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENDOSTATIN


Mass: 18950.355 Da / Num. of mol.: 1
Fragment: C-TERMINAL 184 RESIDUES OF ALPHA1 CHAIN OF COLLAGEN XVIII
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL ALA-PRO-LEU-ALA SEQUENCE INTRODUCED BY THE CLONING PROCESS
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: 293 EBNA CELLS / Organ: KIDNEY / Cell line (production host): 293 EBNA CELLS / Production host: Homo sapiens (human) / References: UniProt: P39061
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNUMBERING SCHEME IS BASED ON THE POSITION IN THE CARBOXY-TERMINAL NON-COLLAGENEOUS (NC1) DOMAIN OF ...NUMBERING SCHEME IS BASED ON THE POSITION IN THE CARBOXY-TERMINAL NON-COLLAGENEOUS (NC1) DOMAIN OF ALPHA1 (XVIII) COLLAGEN; IN THE MOUSE PROTEIN, THIS DOMAIN CONTAINS 315 AMINO ACID RESIDUES; ENDOSTATIN STARTS AT HIS 132 AND STOPS AT THE CARBOXY TERMINUS OF ALPHA1(XVIII) COLLAGEN, LYS 315; ONLY RESIDUES GLN 138 - PHE 309 ARE VISIBLE IN THE ELECTRON DENSITY.

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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: 1.95 Å3/Da / Density % sol: 37 %
Description: THREE DERIVATIVES WERE USED, BEFORE SOLVENT FLATTENING WAS 0.584
Crystal growpH: 5.3 / Details: pH 5.3
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
25 mMMops1reservoir
31.5-1.7 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 17, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 26471 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 5.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.9 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 159011
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS, SOLVENT FLATTENING AT 2.2 A RESOLUTION
Resolution: 1.5→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED INDIVIDUAL B-F / Cross valid method: FREE R-FACTOR / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2634 10 %RANDOM
Rwork0.19 ---
obs0.19 26155 99.5 %-
Displacement parametersBiso mean: 16 Å2
Refine analyzeLuzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 0 83 1416
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.6
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_it3.71
X-RAY DIFFRACTIONx_mcangle_it3.72
X-RAY DIFFRACTIONx_scbond_it3.72
X-RAY DIFFRACTIONx_scangle_it3.74
LS refinement shellResolution: 1.5→1.55 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.229 256 10 %
Rwork0.249 2194 -
obs--99.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.249

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