[English] 日本語
Yorodumi
- PDB-2doi: The X-ray crystallographic structure of the angiogenesis inhibito... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2doi
TitleThe X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcus protein PAM
Components
  • Angiostatin
  • Plasminogen-binding group A streptococcal M-like protein PAM
KeywordsHYDROLASE / plasminogen / kringle domain / lysine-binding site / pseudo-lysine moiety
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / myoblast differentiation / negative regulation of cell-substrate adhesion / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / plasminogen activation / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / kinase binding / Schaffer collateral - CA1 synapse / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / : / Streptococcal M proteins D repeats region profile. / : / Streptococcal M proteins C repeat profile. / Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains ...Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / : / Streptococcal M proteins D repeats region profile. / : / Streptococcal M proteins C repeat profile. / Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / YSIRK Gram-positive signal peptide / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Plasminogen / Plasminogen-binding group A streptococcal M-like protein PAM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCnudde, S.E. / Prorok, M. / Castellino, F.J. / Geiger, J.H.
CitationJournal: Biochemistry / Year: 2006
Title: X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcal surface protein PAM
Authors: Cnudde, S.E. / Prorok, M. / Castellino, F.J. / Geiger, J.H.
History
DepositionApr 29, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Angiostatin
C: Plasminogen-binding group A streptococcal M-like protein PAM
A: Angiostatin
B: Plasminogen-binding group A streptococcal M-like protein PAM


Theoretical massNumber of molelcules
Total (without water)60,7854
Polymers60,7854
Non-polymers00
Water00
1
X: Angiostatin
C: Plasminogen-binding group A streptococcal M-like protein PAM


Theoretical massNumber of molelcules
Total (without water)30,3932
Polymers30,3932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Angiostatin
B: Plasminogen-binding group A streptococcal M-like protein PAM


Theoretical massNumber of molelcules
Total (without water)30,3932
Polymers30,3932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.467, 58.467, 389.146
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Angiostatin


Mass: 26757.619 Da / Num. of mol.: 2 / Fragment: Kringle 1,Kringle 2 and Kringle 3 / Mutation: N289E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Pichia pastoris (fungus) / References: UniProt: P00747, plasmin
#2: Protein/peptide Plasminogen-binding group A streptococcal M-like protein PAM


Mass: 3635.021 Da / Num. of mol.: 2 / Fragment: VEK-30 / Source method: obtained synthetically
Details: VEK-30 is an internal peptide within the streptococcus protein PAM
References: UniProt: P49054
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 8000, 0.1M potassium phophate (dihydrate), 5% dioxane, soaked in 5mM Pt(C5H5N)2Cl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.0719 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0719 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15828 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.086 / Χ2: 1.776 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.507 / Num. unique all: 410 / Χ2: 0.824 / % possible all: 22.2

-
Phasing

Phasing MRRfactor: 0.356 / Cor.coef. Fo:Fc: 0.661
Highest resolutionLowest resolution
Rotation3.5 Å19.96 Å
Translation3.5 Å19.96 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2DOH

2doh


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.839 / SU B: 47.539 / SU ML: 0.386 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.683 / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 675 5.1 %RANDOM
Rwork0.202 ---
all0.206 ---
obs0.202 13107 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.457 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20.89 Å20 Å2
2--1.78 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 0 0 3064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0213157
X-RAY DIFFRACTIONr_angle_refined_deg2.5931.9494277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6145375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81824.217166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.16115538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.71526
X-RAY DIFFRACTIONr_chiral_restr0.1550.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022476
X-RAY DIFFRACTIONr_nbd_refined0.380.32119
X-RAY DIFFRACTIONr_nbtor_refined0.3720.52056
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3350.5237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.360
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4570.56
X-RAY DIFFRACTIONr_mcbond_it15.8271.51969
X-RAY DIFFRACTIONr_mcangle_it19.52623077
X-RAY DIFFRACTIONr_scbond_it30.59131398
X-RAY DIFFRACTIONr_scangle_it32.9574.51200
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 48 -
Rwork0.24 823 -
obs-871 91.59 %
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)
10.9476-2.29261.39846.2745-4.02152.62340.0109-0.22980.1965-0.0104-0.0103-0.2917-0.2869-0.1026-0.00050.25320.25520.09830.0744-0.0095-0.033-0.193147.2740.943
22.5072-3.0001-2.40173.94052.82432.3077-0.10140.0465-0.03630.00030.15260.33-0.1023-0.0812-0.05130.2750.18240.06270.00660.07520.015217.892323.8387-26.8743
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11XA81 - 2981 - 218
21CB303 - 3263 - 26
32AC81 - 2441 - 164
42BD304 - 3274 - 27

+
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