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- PDB-4iml: CrossFab binding to human Angiopoietin 2 -

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Basic information

Entry
Database: PDB / ID: 4iml
TitleCrossFab binding to human Angiopoietin 2
Components
  • Crossed heavy chain (VH-Ckappa)
  • Crossed light chain (VL-CH1)
KeywordsIMMUNE SYSTEM / CrossFab / antigen binding / human Angiopoietin 2
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.931 Å
AuthorsFenn, S. / Schiller, C. / Griese, J. / Hopfner, K.-P. / Kettenberger, H.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structure of an Anti-Ang2 CrossFab Demonstrates Complete Structural and Functional Integrity of the Variable Domain.
Authors: Fenn, S. / Schiller, C.B. / Griese, J.J. / Duerr, H. / Imhof-Jung, S. / Gassner, C. / Moelleken, J. / Regula, J.T. / Schaefer, W. / Thomas, M. / Klein, C. / Hopfner, K.P. / Kettenberger, H.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Crossed heavy chain (VH-Ckappa)
L: Crossed light chain (VL-CH1)
A: Crossed heavy chain (VH-Ckappa)
B: Crossed light chain (VL-CH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7796
Polymers98,5954
Non-polymers1842
Water1267
1
H: Crossed heavy chain (VH-Ckappa)
L: Crossed light chain (VL-CH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3903
Polymers49,2972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-24 kcal/mol
Surface area20250 Å2
MethodPISA
2
A: Crossed heavy chain (VH-Ckappa)
B: Crossed light chain (VL-CH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3903
Polymers49,2972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-25 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.755, 80.552, 158.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain H and (resseq 1:232 ) and (not element H) and (not element D)
211chain A and (resseq 1:232 ) and (not element H) and (not element D)
112chain L and (resseq 2:210 ) and (not element H) and (not element D)
212chain B and (resseq 2:210 ) and (not element H) and (not element D)

NCS ensembles :
ID
1
2

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Components

#1: Antibody Crossed heavy chain (VH-Ckappa)


Mass: 27083.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Crossed light chain (VL-CH1)


Mass: 22213.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 17.5-20 %(w/v) PEG6000, 0.1 M citric acid, 0.2 M NDSB-221, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.795→44.133 Å / Num. obs: 24225

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.931→44.133 Å / SU ML: 0.42 / σ(F): 2.03 / Phase error: 32.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 1060 5.01 %
Rwork0.237 --
obs0.2387 21156 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.8085 Å20 Å20 Å2
2---9.0101 Å20 Å2
3---2.2016 Å2
Refinement stepCycle: LAST / Resolution: 2.931→44.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 12 7 6743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036914
X-RAY DIFFRACTIONf_angle_d0.8639412
X-RAY DIFFRACTIONf_dihedral_angle_d13.9162453
X-RAY DIFFRACTIONf_chiral_restr0.0581038
X-RAY DIFFRACTIONf_plane_restr0.0041214
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11H1792X-RAY DIFFRACTIONPOSITIONAL
12A1792X-RAY DIFFRACTIONPOSITIONAL0.085
21L1531X-RAY DIFFRACTIONPOSITIONAL
22B1531X-RAY DIFFRACTIONPOSITIONAL0.071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9309-3.06420.34371190.34122247X-RAY DIFFRACTION90
3.0642-3.22570.37621310.29872497X-RAY DIFFRACTION100
3.2257-3.42780.31731330.26822515X-RAY DIFFRACTION100
3.4278-3.69230.25841330.24212507X-RAY DIFFRACTION100
3.6923-4.06360.28561330.23742524X-RAY DIFFRACTION100
4.0636-4.65110.21711340.19442545X-RAY DIFFRACTION100
4.6511-5.85770.2631350.20442579X-RAY DIFFRACTION100
5.8577-44.13780.24311420.23882682X-RAY DIFFRACTION99

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