[English] 日本語
Yorodumi
- PDB-1koe: ENDOSTATIN -

+
Open data


ID or keywords:

Loading...

-
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


Activation of Matrix Metalloproteinases / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / vascular endothelial cell proliferation / blood vessel endothelial cell migration / Integrin cell surface interactions / endothelial cell morphogenesis / collagen trimer ...Activation of Matrix Metalloproteinases / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / vascular endothelial cell proliferation / blood vessel endothelial cell migration / Integrin cell surface interactions / endothelial cell morphogenesis / collagen trimer / endothelial cell apoptotic process / positive regulation of vascular endothelial cell proliferation / basement membrane / positive regulation of endothelial cell apoptotic process / positive regulation of blood vessel endothelial cell migration / extracellular matrix organization / : / angiogenesis / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more