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- PDB-2doi: The X-ray crystallographic structure of the angiogenesis inhibito... -

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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 / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / plasminogen activation / 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 / Schaffer collateral - CA1 synapse / kinase binding / 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 / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Streptococcal M proteins C repeat profile. / Streptococcal M proteins D repeats region profile. / Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain ...Streptococcal M proteins C repeat profile. / Streptococcal M proteins D repeats region profile. / Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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

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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: 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

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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

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Phasing

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

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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

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