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- PDB-4zfg: Dual-specificity Fab 5A12 in complex with Angiopoietin 2 -

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Basic information

Entry
Database: PDB / ID: 4zfg
TitleDual-specificity Fab 5A12 in complex with Angiopoietin 2
Components
  • (Fragment antigen binding 5A12 ...) x 2
  • Angiopoietin-2Angiopoietin
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Fab / DAF / angiogenesis / Tie receptor / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of positive chemotaxis / Tie signaling pathway / glomerulus vasculature development / negative regulation of cell-substrate adhesion / germ cell development / negative regulation of blood vessel endothelial cell migration / maternal process involved in female pregnancy / animal organ regeneration / response to glucose / response to mechanical stimulus ...negative regulation of positive chemotaxis / Tie signaling pathway / glomerulus vasculature development / negative regulation of cell-substrate adhesion / germ cell development / negative regulation of blood vessel endothelial cell migration / maternal process involved in female pregnancy / animal organ regeneration / response to glucose / response to mechanical stimulus / Tie2 Signaling / negative regulation of angiogenesis / response to activity / cell projection / response to organic cyclic compound / receptor tyrosine kinase binding / cellular response to growth factor stimulus / positive regulation of angiogenesis / gene expression / angiogenesis / collagen-containing extracellular matrix / response to hypoxia / signaling receptor binding / signal transduction / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Few Secondary Structures / Irregular / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsHarris, S.F. / Wu, P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Deep Sequencing-guided Design of a High Affinity Dual Specificity Antibody to Target Two Angiogenic Factors in Neovascular Age-related Macular Degeneration.
Authors: Koenig, P. / Lee, C.V. / Sanowar, S. / Wu, P. / Stinson, J. / Harris, S.F. / Fuh, G.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiopoietin-2
H: Fragment antigen binding 5A12 heavy chain
L: Fragment antigen binding 5A12 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4838
Polymers74,0593
Non-polymers4245
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-104 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.668, 109.292, 43.946
Angle α, β, γ (deg.)90.00, 100.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-430-

HOH

21H-541-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Angiopoietin-2 / Angiopoietin / ANG-2


Mass: 26530.371 Da / Num. of mol.: 1 / Fragment: Receptor binding domain, UNP residues 225-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANGPT2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O15123

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fragment antigen binding 5A12 heavy chain


Mass: 24231.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Fragment antigen binding 5A12 light chain


Mass: 23296.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 402 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M lithium sulfate, 25% PEG 3350, 3% D(+)-sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2011
RadiationMonochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 38887 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 53.21 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.045
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.27-2.353.80.54238641.01999.1
2.35-2.453.90.43738591.03199.2
2.45-2.563.90.31738741.0799.3
2.56-2.693.90.21538581.07999.4
2.69-2.863.90.14738661.09499.5
2.86-3.083.90.09438831.09499.7
3.08-3.393.90.06539091.01399.7
3.39-3.883.90.04938901.06699.8
3.88-4.893.80.03739341.01499.7
4.89-503.80.03339501.04899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house ang2 and generic fab models

Resolution: 2.27→43.21 Å / Cor.coef. Fo:Fc: 0.9319 / Cor.coef. Fo:Fc free: 0.9089 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.232 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.189
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 1947 5.02 %RANDOM
Rwork0.1771 ---
obs0.1794 38814 99.48 %-
Displacement parametersBiso mean: 59.9 Å2
Baniso -1Baniso -2Baniso -3
1-21.0074 Å20 Å23.5313 Å2
2---17.0857 Å20 Å2
3----3.9217 Å2
Refine analyzeLuzzati coordinate error obs: 0.276 Å
Refinement stepCycle: LAST / Resolution: 2.27→43.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 21 397 5445
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015175HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.137032HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1706SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes112HARMONIC2
X-RAY DIFFRACTIONt_gen_planes758HARMONIC5
X-RAY DIFFRACTIONt_it5175HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion661SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6141SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.33 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2427 140 4.66 %
Rwork0.2254 2864 -
all0.2263 3004 -
obs--99.48 %

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