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- PDB-4imk: Uncrossed Fab binding to human Angiopoietin 2 -

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Basic information

Entry
Database: PDB / ID: 4imk
TitleUncrossed Fab binding to human Angiopoietin 2
Components
  • Heavy Chain
  • Light Chain
KeywordsIMMUNE SYSTEM / antigen-binding fragment (Fab) / 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: 2.202 Å
AuthorsFenn, S. / Schiller, C. / Griese, J.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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy Chain
B: Heavy Chain
C: Light Chain
D: Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3708
Polymers98,0674
Non-polymers3034
Water5,747319
1
A: Heavy Chain
D: Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1484
Polymers49,0332
Non-polymers1152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-36 kcal/mol
Surface area19250 Å2
MethodPISA
2
B: Heavy Chain
C: Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2214
Polymers49,0332
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-34 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.969, 86.670, 205.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules ABCD

#1: Antibody Heavy Chain


Mass: 24771.711 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 Light Chain


Mass: 24261.551 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)

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Non-polymers , 4 types, 323 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15%(w/v) PEG4000, 0.1 M Tri-Na-citrate, 15%(v/v) isopropanol, pH 7.0, 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: 2.2→46.761 Å / Num. obs: 60561

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.202→46.761 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 3029 5 %
Rwork0.199 --
obs0.2003 60561 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→46.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6690 0 18 319 7027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036882
X-RAY DIFFRACTIONf_angle_d0.8249368
X-RAY DIFFRACTIONf_dihedral_angle_d13.7322444
X-RAY DIFFRACTIONf_chiral_restr0.0561033
X-RAY DIFFRACTIONf_plane_restr0.0041207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2015-2.23590.32741300.3132454X-RAY DIFFRACTION96
2.2359-2.27260.36841370.28112615X-RAY DIFFRACTION100
2.2726-2.31180.31531330.26552534X-RAY DIFFRACTION100
2.3118-2.35380.2961390.26032631X-RAY DIFFRACTION100
2.3538-2.39910.31481350.26622563X-RAY DIFFRACTION100
2.3991-2.4480.29411370.24872596X-RAY DIFFRACTION100
2.448-2.50130.30491340.25742555X-RAY DIFFRACTION100
2.5013-2.55950.33771370.24242602X-RAY DIFFRACTION100
2.5595-2.62350.27821370.24172607X-RAY DIFFRACTION100
2.6235-2.69440.28941360.24632576X-RAY DIFFRACTION100
2.6944-2.77370.27451390.23252638X-RAY DIFFRACTION100
2.7737-2.86320.26941370.23652604X-RAY DIFFRACTION100
2.8632-2.96550.25971350.23132575X-RAY DIFFRACTION100
2.9655-3.08420.25331380.22972611X-RAY DIFFRACTION100
3.0842-3.22450.26591380.22152630X-RAY DIFFRACTION100
3.2245-3.39450.22121380.21342617X-RAY DIFFRACTION100
3.3945-3.60710.21791390.19442642X-RAY DIFFRACTION100
3.6071-3.88550.19651390.1882644X-RAY DIFFRACTION100
3.8855-4.27620.19561380.17032624X-RAY DIFFRACTION100
4.2762-4.89440.16361410.14862679X-RAY DIFFRACTION100
4.8944-6.16430.20541420.17552697X-RAY DIFFRACTION100
6.1643-46.77110.20141500.18472838X-RAY DIFFRACTION100

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