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- PDB-1wq8: Crystal structure of Vammin, a VEGF-F from a snake venom -

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Basic information

Entry
Database: PDB / ID: 1wq8
TitleCrystal structure of Vammin, a VEGF-F from a snake venom
ComponentsVascular endothelial growth factor toxin
KeywordsTOXIN / snake venom / Vascular endothelial growth factor / VEGF / VEGF-F
Function / homology
Function and homology information


vascular endothelial growth factor receptor binding / positive regulation of mast cell chemotaxis / induction of positive chemotaxis / sprouting angiogenesis / vascular endothelial growth factor signaling pathway / chemoattractant activity / vascular endothelial growth factor receptor signaling pathway / positive regulation of endothelial cell proliferation / growth factor activity / positive regulation of angiogenesis ...vascular endothelial growth factor receptor binding / positive regulation of mast cell chemotaxis / induction of positive chemotaxis / sprouting angiogenesis / vascular endothelial growth factor signaling pathway / chemoattractant activity / vascular endothelial growth factor receptor signaling pathway / positive regulation of endothelial cell proliferation / growth factor activity / positive regulation of angiogenesis / toxin activity / response to hypoxia / extracellular space / membrane
Similarity search - Function
: / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine ...: / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Snake venom vascular endothelial growth factor toxin vammin / Snake venom vascular endothelial growth factor toxin HF
Similarity search - Component
Biological speciesVipera aspis aspis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSuto, K. / Yamazaki, Y. / Morita, T. / Mizuno, H.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Crystal structures of novel vascular endothelial growth factors (VEGF) from snake venoms: insight into selective VEGF binding to kinase insert domain-containing receptor but not to fms-like tyrosine kinase-1.
Authors: Suto, K. / Yamazaki, Y. / Morita, T. / Mizuno, H.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Snake venom vascular endothelial growth factors (VEGFs) exhibit potent activity through their specific recognition of KDR (VEGF receptor 2)
Authors: Yamazaki, Y. / Takani, K. / Atoda, H. / Morita, T.
History
DepositionSep 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vascular endothelial growth factor toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6982
Polymers12,5751
Non-polymers1221
Water3,099172
1
A: Vascular endothelial growth factor toxin
hetero molecules

A: Vascular endothelial growth factor toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3954
Polymers25,1512
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3370 Å2
ΔGint-11 kcal/mol
Surface area12220 Å2
MethodPISA
2
A: Vascular endothelial growth factor toxin
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)101,58116
Polymers100,6048
Non-polymers9778
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area20430 Å2
ΔGint-60 kcal/mol
Surface area41940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.526, 85.526, 86.365
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1021-

HOH

21A-1069-

HOH

31A-1168-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis:y, x, -z

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Components

#1: Protein Vascular endothelial growth factor toxin / VR-1 / VEGF-F


Mass: 12575.499 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vipera aspis aspis (snake) / Secretion: venom / Species: Vipera aspis / Strain: aspis / References: UniProt: P83942, UniProt: P67863*PLUS
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: PEG 6000, Tris-HCl, glycerol, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2003
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 13068 / Num. obs: 12903 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.218 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VR-1

Resolution: 1.9→23 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1706273.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 648 5 %RANDOM
Rwork0.192 ---
obs0.192 12885 99.5 %-
all-12927 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.5954 Å2 / ksol: 0.377209 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms791 0 8 172 971
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.692
X-RAY DIFFRACTIONc_scangle_it3.962.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 122 5.9 %
Rwork0.196 1961 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BUFFER.PARAMBUFFER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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