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Basic information

Entry
Database: PDB / ID: 2doh
TitleThe X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound a to a peptide from the group A streptococcal surface protein PAM
Components
  • Angiostatin
  • Plasminogen-binding group A streptococcal M-like protein PAM
KeywordsHYDROLASE / lysine-binding site / plasminogen / kringle domains
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
1,4-DIETHYLENE DIOXIDE / Plasminogen / Plasminogen-binding group A streptococcal M-like protein PAM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / Refinement description / Version format compliance
Revision 1.3Oct 5, 2011Group: Derived calculations
Revision 1.4Oct 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 1.5Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4653
Polymers30,3772
Non-polymers881
Water5,603311
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.377, 58.377, 391.033
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-356-

HOH

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Components

#1: Protein Angiostatin /


Mass: 26757.619 Da / Num. of mol.: 1 / 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 / Fragment


Mass: 3618.999 Da / Num. of mol.: 1 / Fragment: VEK-30 / Source method: obtained synthetically / Details: VEK-30 is an internal peptide within PAM / References: UniProt: P49054*PLUS
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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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: 61.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 8000, 0.1M potassium phosphate (dihydrate), 5% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 12.4 / Number: 320127 / Rmerge(I) obs: 0.091 / Χ2: 2.53 / D res high: 2 Å / D res low: 50 Å / Num. obs: 22779 / % possible obs: 80.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.315088.610.0714.129
3.424.3197.210.0823.817
2.993.4210010.1022.608
2.712.9910010.1362.01
2.522.7199.510.1881.868
2.372.5290.110.2311.259
2.252.3778.710.3781.052
2.152.2568.110.5121.073
2.072.1556.410.8120.752
22.0719.110.8341.484
ReflectionResolution: 2→50 Å / Num. obs: 22779 / % possible obs: 80.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.091 / Χ2: 2.525 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.834 / Num. unique all: 524 / Χ2: 1.484 / % possible all: 19.1

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Phasing

Phasing MRRfactor: 0.406 / Cor.coef. Fo:Fc: 0.738
Highest resolutionLowest resolution
Rotation2.5 Å19.97 Å
Translation2.5 Å19.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KI0

1ki0


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.339 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1775 10.1 %RANDOM
Rwork0.21 ---
all0.215 ---
obs0.21 17617 93.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.651 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20.79 Å20 Å2
2--1.57 Å20 Å2
3----2.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 6 311 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211595
X-RAY DIFFRACTIONr_bond_other_d0.0050.021312
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9522155
X-RAY DIFFRACTIONr_angle_other_deg1.55733121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1875186
X-RAY DIFFRACTIONr_chiral_restr0.0790.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021760
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02303
X-RAY DIFFRACTIONr_nbd_refined0.2610.3449
X-RAY DIFFRACTIONr_nbd_other0.2760.31725
X-RAY DIFFRACTIONr_nbtor_other0.0990.5847
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3370.5293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3440.361
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4280.531
X-RAY DIFFRACTIONr_mcbond_it1.4051.5949
X-RAY DIFFRACTIONr_mcangle_it2.27921539
X-RAY DIFFRACTIONr_scbond_it3.5163646
X-RAY DIFFRACTIONr_scangle_it4.744.5616
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.328 95
Rwork0.3 894
obs-989
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)
18.3696-1.38750.12071.9201-0.35723.8554-0.1019-0.5894-0.42260.07710.05810.00980.0971-0.02630.04380.0429-0.03930.02180.35120.13970.1577-0.089921.98245.1946
23.84310.00811.68872.9564-1.38897.694-0.00840.37470.2679-0.06360.030.2135-0.12790.0092-0.02160.0493-0.02170.01180.28470.02710.082329.689723.005317.5897
335.072210.24481.71289.9301-1.049611.5063-0.11450.1063-0.06290.17620.0224-0.0095-0.5842-0.04380.0920.27930.030.04860.13350.01340.0130.40725.45231.8573
42.24070.13221.00890.2801-0.22240.99710.00040.02010.10.1250.02440.063-0.0264-0.0828-0.02480.28440.00270.04640.4950.03280.319715.701520.981414.5417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X81 - 164
2X-RAY DIFFRACTION1X1001
3X-RAY DIFFRACTION2X165 - 245
4X-RAY DIFFRACTION3C304 - 326
5X-RAY DIFFRACTION3C328
6X-RAY DIFFRACTION4C331 - 375
7X-RAY DIFFRACTION4X1002 - 1267

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