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- PDB-4glu: Crystal structure of the mirror image form of VEGF-A -

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Basic information

Entry
Database: PDB / ID: 4glu
TitleCrystal structure of the mirror image form of VEGF-A
ComponentsD- Vascular endothelial growth factor-A
KeywordsDE NOVO PROTEIN / D-protein / covalent dimer / cysteine knot protein / growth factor
Function / homologyACETATE ION / trifluoroacetic acid / polypeptide(D) / polypeptide(D) (> 10) / polypeptide(D) (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMandal, K. / Uppalapati, M. / Ault-Riche, D. / Kenney, J. / Lowitz, J. / Sidhu, S. / Kent, S.B.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography.
Authors: Mandal, K. / Uppalapati, M. / Ault-Riche, D. / Kenney, J. / Lowitz, J. / Sidhu, S.S. / Kent, S.B.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D- Vascular endothelial growth factor-A
D: D- Vascular endothelial growth factor-A
B: D- Vascular endothelial growth factor-A
C: D- Vascular endothelial growth factor-A
E: D- Vascular endothelial growth factor-A
F: D- Vascular endothelial growth factor-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,41327
Polymers71,6566
Non-polymers1,75721
Water6,828379
1
A: D- Vascular endothelial growth factor-A
D: D- Vascular endothelial growth factor-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,61110
Polymers23,8852
Non-polymers7258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-27 kcal/mol
Surface area11160 Å2
MethodPISA
2
B: D- Vascular endothelial growth factor-A
C: D- Vascular endothelial growth factor-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4209
Polymers23,8852
Non-polymers5347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-27 kcal/mol
Surface area11550 Å2
MethodPISA
3
E: D- Vascular endothelial growth factor-A
F: D- Vascular endothelial growth factor-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3838
Polymers23,8852
Non-polymers4976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-29 kcal/mol
Surface area11400 Å2
MethodPISA
4
A: D- Vascular endothelial growth factor-A
D: D- Vascular endothelial growth factor-A
hetero molecules

B: D- Vascular endothelial growth factor-A
C: D- Vascular endothelial growth factor-A
E: D- Vascular endothelial growth factor-A
F: D- Vascular endothelial growth factor-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,41327
Polymers71,6566
Non-polymers1,75721
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
identity operation1_555x,y,z1
Buried area14580 Å2
ΔGint-98 kcal/mol
Surface area30830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.395, 43.986, 73.514
Angle α, β, γ (deg.)90.00, 100.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
D- Vascular endothelial growth factor-A


Mass: 11942.639 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M NH4OAc, 0.1 M BIS-TRIS (pH 5.5), 45% (v/v) 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 57494 / Num. obs: 57494 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.16
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2889 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1128)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QTK

3qtk


Resolution: 1.9→32.499 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 2896 5.04 %
Rwork0.1725 --
obs0.1743 57481 98 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 113 379 5154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074933
X-RAY DIFFRACTIONf_angle_d1.1466617
X-RAY DIFFRACTIONf_dihedral_angle_d15.2521946
X-RAY DIFFRACTIONf_chiral_restr0.078679
X-RAY DIFFRACTIONf_plane_restr0.005883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92410.30351340.25282297X-RAY DIFFRACTION88
1.9241-1.95720.28931280.23512607X-RAY DIFFRACTION100
1.9572-1.99280.2731420.2232682X-RAY DIFFRACTION100
1.9928-2.03110.2251460.20722533X-RAY DIFFRACTION99
2.0311-2.07260.26881370.20272637X-RAY DIFFRACTION99
2.0726-2.11760.2631270.19282633X-RAY DIFFRACTION100
2.1176-2.16690.25531380.19642617X-RAY DIFFRACTION99
2.1669-2.22110.22321300.18412629X-RAY DIFFRACTION99
2.2211-2.28110.22491680.18112560X-RAY DIFFRACTION99
2.2811-2.34820.19931350.17622636X-RAY DIFFRACTION99
2.3482-2.4240.23811360.17462620X-RAY DIFFRACTION99
2.424-2.51060.23671510.17522600X-RAY DIFFRACTION99
2.5106-2.61110.23641510.17692648X-RAY DIFFRACTION99
2.6111-2.72990.22621350.17282607X-RAY DIFFRACTION99
2.7299-2.87370.24531290.17422597X-RAY DIFFRACTION99
2.8737-3.05360.22391280.16652605X-RAY DIFFRACTION98
3.0536-3.28920.21141330.15272613X-RAY DIFFRACTION98
3.2892-3.61980.17721450.152602X-RAY DIFFRACTION98
3.6198-4.14270.17761350.14392606X-RAY DIFFRACTION97
4.1427-5.21580.15751510.14762621X-RAY DIFFRACTION97
5.2158-32.4990.20711170.2022635X-RAY DIFFRACTION94
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)
10.82540.09081.11461.1910.40564.5122-0.01680.0261-0.02590.053-0.07020.05610.0140.05330.09530.13980.0113-0.00720.1123-0.02090.2036-33.68220.25818.6498
22.0662-0.44410.56721.30760.48252.98470.15550.3712-0.27720.03850.0496-0.08760.4970.5836-0.16670.21940.08-0.01210.2263-0.01860.2331-25.06829.520810.0997
31.52580.32580.88160.42290.73782.47140.093-0.14480.03040.14430.0219-0.00560.15940.0288-0.14260.19730.0203-0.02240.10140.00260.2259-53.8862-7.708516.3969
42.19220.10110.27291.12551.18424.31570.06-0.52510.31410.1045-0.15480.0595-0.1746-0.66520.02070.22230.03430.04160.2181-0.05330.3108-60.86964.182523.5018
53.20310.78681.01171.05580.04712.7470.1348-0.5487-0.11420.308-0.1402-0.0130.022-0.33890.03480.2702-0.07380.02390.25050.02480.1864-32.8538-10.305956.1226
62.87830.58381.01890.90720.25062.1569-0.07160.06880.27010.0789-0.0637-0.0039-0.29840.31860.18820.2792-0.1092-0.01030.22820.04220.1895-21.5173-0.093450.9409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'D'
3X-RAY DIFFRACTION3chain 'B'
4X-RAY DIFFRACTION4chain 'C'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'

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