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- PDB-2gnn: Crystal Structure of the Orf Virus NZ2 Variant of VEGF-E -

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Basic information

Entry
Database: PDB / ID: 2gnn
TitleCrystal Structure of the Orf Virus NZ2 Variant of VEGF-E
ComponentsVascular endothelial growth factor homolog
KeywordsHORMONE/GROWTH FACTOR / VEGF / Orf / S-SAD / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


vascular endothelial growth factor receptor binding / positive regulation of mast cell chemotaxis / induction of positive chemotaxis / sprouting angiogenesis / chemoattractant activity / positive regulation of cell division / positive regulation of endothelial cell proliferation / growth factor activity / positive regulation of angiogenesis / response to hypoxia ...vascular endothelial growth factor receptor binding / positive regulation of mast cell chemotaxis / induction of positive chemotaxis / sprouting angiogenesis / chemoattractant activity / positive regulation of cell division / positive regulation of endothelial cell proliferation / growth factor activity / positive regulation of angiogenesis / response to hypoxia / positive regulation of protein phosphorylation / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
BENZAMIDINE / Vascular endothelial growth factor homolog
Similarity search - Component
Biological speciesOrf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsProta, A.E. / Pieren, M. / Wagner, A. / Kostrewa, D. / Winkler, F.K. / Ballmer-Hofer, K.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Crystal structure of the Orf virus NZ2 variant of vascular endothelial growth factor-E. Implications for receptor specificity.
Authors: Pieren, M. / Prota, A.E. / Ruch, C. / Kostrewa, D. / Wagner, A. / Biedermann, K. / Winkler, F.K. / Ballmer-Hofer, K.
#1: Journal: To be Published
Title: Sulfur SAD at low resolution - Structure Determination of VEGF-E
Authors: Wagner, A. / Pieren, M. / Kostrewa, D. / Schulze-Briese, C. / Ballmer-Hofer, K. / Prota, A.E.
History
DepositionApr 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE Sequence in the entry is in accordance with Lyttle et al., J.Virol. 68, 1994, p.84-92

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vascular endothelial growth factor homolog
B: Vascular endothelial growth factor homolog
C: Vascular endothelial growth factor homolog
D: Vascular endothelial growth factor homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,17524
Polymers57,0924
Non-polymers2,08220
Water3,189177
1
A: Vascular endothelial growth factor homolog
B: Vascular endothelial growth factor homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,90615
Polymers28,5462
Non-polymers1,36013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-22 kcal/mol
Surface area12710 Å2
MethodPISA
2
C: Vascular endothelial growth factor homolog
D: Vascular endothelial growth factor homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2699
Polymers28,5462
Non-polymers7237
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-35 kcal/mol
Surface area11870 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-57 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.600, 98.600, 240.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsTwo biologically active, disulfide linked homodimers are present in the asymmetric unit

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

#1: Protein
Vascular endothelial growth factor homolog


Mass: 14273.079 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orf virus (strain NZ2) / Genus: Parapoxvirus / Species: Orf virus / Strain: NZ2 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P52584
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 195 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2

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Sample preparation

CrystalDensity Matthews: 5.10419 Å3/Da / Density % sol: 75.902153 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.6 M Ammonium sulfate, 3% PEG 4K, 0.1 M Sodium citrate, 0.3% Benzamidine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11.00017
SYNCHROTRONSLS X06SA21.698383
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJul 27, 2004
MAR CCD 165 mm2CCDJul 31, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED SI(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.000171
21.6983831
ReflectionAv σ(I) over netI: 30.11 / Number: 678251 / Rmerge(I) obs: 0.081 / D res high: 3 Å / Num. obs: 44146 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1048113899.910.027
610442099.910.038
56406099.410.049
45921599.410.059
3.84313999.410.087
3.73.818139910.103
3.63.7202198.910.136
3.53.6224997.810.154
3.43.5251797.310.192
3.33.4275495.210.254
3.23.3319297.410.309
33.2756495.710.456
ReflectionResolution: 2.3→48.48 Å / Num. obs: 52820 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 57.637 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.58
Reflection shellResolution: 2.3→2.4 Å / % possible obs: 85.4 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 3.1 / Num. measured obs: 39132 / Num. unique all: 6199 / Num. unique obs: 5379 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
MAR345data collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.48 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.765 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.145 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2687 5.1 %RANDOM
Rwork0.223 ---
all0.224 ---
obs0.224 52820 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.047 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2--1.93 Å20 Å2
3----3.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2831 0 132 177 3140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223021
X-RAY DIFFRACTIONr_angle_refined_deg1.252.0194074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0525363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61924.38121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60115520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6281523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022198
X-RAY DIFFRACTIONr_nbd_refined0.1990.21147
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.222
X-RAY DIFFRACTIONr_mcbond_it2.07521909
X-RAY DIFFRACTIONr_mcangle_it3.34733037
X-RAY DIFFRACTIONr_scbond_it5.2934.51203
X-RAY DIFFRACTIONr_scangle_it7.72561037
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 180 -
Rwork0.314 3644 -
obs-3824 98.53 %
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)
18.44672.1087-0.25722.7233-0.99675.06950.12610.481-0.429-0.34690.31830.32920.306-1.2029-0.4444-0.22150.0049-0.10560.09970.0469-0.264616.289361.031717.1659
210.70972.9102-0.63292.3802-0.30541.48630.12010.48040.096-0.11830.16020.3088-0.2477-0.9592-0.2803-0.18620.0986-0.03550.11150.0935-0.322121.227968.92223.9264
37.55991.4297-2.72683.47050.72826.48730.4866-1.15740.2640.30490.1261-0.7003-0.65261.6912-0.61270.0231-0.23560.01260.0884-0.176-0.152464.134880.826912.7494
49.56193.437-2.46093.5629-0.47083.72450.3691-0.82110.63260.1550.0753-0.432-0.99191.2021-0.44440.0875-0.2630.06830.0324-0.2487-0.156855.098483.504625.7727
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA11 - 1097 - 105
22BB13 - 1079 - 103
33CC11 - 1107 - 106
44DD14 - 10610 - 102

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