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- PDB-2r0z: PFA1 FAB complexed with GripI peptide fragment -

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Basic information

Entry
Database: PDB / ID: 2r0z
TitlePFA1 FAB complexed with GripI peptide fragment
Components
  • GripI peptide fragment
  • IgG2a Fab fragment heavy chain, Fd portion
  • IgG2a Fab fragment light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / Alzheimer disease / amyloid
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.096 Å
AuthorsGardberg, A.S. / Dealwis, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular basis for passive immunotherapy of Alzheimer's disease
Authors: Gardberg, A.S. / Dice, L.T. / Ou, S. / Rich, R.L. / Helmbrecht, E. / Ko, J. / Wetzel, R. / Myszka, D.G. / Patterson, P.H. / Dealwis, C.
History
DepositionAug 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IgG2a Fab fragment light chain
H: IgG2a Fab fragment heavy chain, Fd portion
Q: GripI peptide fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1685
Polymers48,9843
Non-polymers1842
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.467, 112.243, 43.174
Angle α, β, γ (deg.)90.000, 93.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody IgG2a Fab fragment light chain


Mass: 24203.863 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3
#2: Antibody IgG2a Fab fragment heavy chain, Fd portion


Mass: 24003.918 Da / Num. of mol.: 1 / Fragment: Fd portion of heavy chain / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide GripI peptide fragment / glutamate receptor interacting protein 1


Mass: 775.875 Da / Num. of mol.: 1 / Fragment: hexapeptide / Source method: obtained synthetically
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: PEG, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
21001
11
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.54178
SYNCHROTRONAPS 14-BM-C20.9
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJul 28, 2006
ADSC QUANTUM 3152CCDAug 11, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
20.91
ReflectionResolution: 2.096→40 Å / Num. obs: 20023 / % possible obs: 87.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.162 / Χ2: 1.259 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.096-2.182.80.223151311,265.6
2.18-2.262.90.2215271.2791,268
2.26-2.372.90.20516721.1011,273.8
2.37-2.492.90.17918181.2191,279.7
2.49-2.653.60.29620451.2761,290.3
2.65-2.855.90.37622841.3131,299.9
2.85-3.1460.26322901.2521,2100
3.14-3.595.80.20522881.4641,299.9
3.59-4.524.80.13122691.1651,299.2
4.52-405.90.10623171.1951,299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.096→33.31 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.867 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. KABAT NUMBERING SCHEME IMPOSED FOLLOWING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1000 5 %RANDOM
Rwork0.201 ---
obs0.204 19995 86.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.002 Å2
Baniso -1Baniso -2Baniso -3
1-4.58 Å20 Å20.15 Å2
2---3.01 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.096→33.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 12 113 3511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223489
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9544753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78923.684133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83515551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9311516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022604
X-RAY DIFFRACTIONr_nbd_refined0.1910.21387
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.29
X-RAY DIFFRACTIONr_mcbond_it0.4211.52257
X-RAY DIFFRACTIONr_mcangle_it0.71223572
X-RAY DIFFRACTIONr_scbond_it1.03531433
X-RAY DIFFRACTIONr_scangle_it1.594.51179
LS refinement shellResolution: 2.096→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 52 -
Rwork0.262 907 -
all-959 -
obs--56.35 %
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)
12.3160.6854-1.08333.3577-1.50012.5055-0.03630.0220.1101-0.19030.097-0.1220.12640.0753-0.0607-0.10730.0393-0.0426-0.04450.015-0.091411.84218.38320.195
21.50350.0732-0.11325.44850.97513.39970.14670.0265-0.11330.52080.02550.05580.3124-0.0587-0.1722-0.1330.0032-0.0675-0.10750.0497-0.09053.372.86133.46
30.69810.7160.15136.47811.44662.02510.040.04030.0774-0.3035-0.09540.15480.1046-0.10120.05540.05450.02550.0086-0.09770.0016-0.174125.425-9.2040.858
42.31451.0541-1.88194.1613-1.56324.8394-0.12970.0311-0.0306-0.0885-0.0444-0.25360.02820.30160.17410.02520.0099-0.0681-0.0851-0.0044-0.12631.102-15.7614.52
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1111 - 117
2X-RAY DIFFRACTION2HB1 - 1231 - 133
3X-RAY DIFFRACTION3LA112 - 213118 - 219
4X-RAY DIFFRACTION4HB124 - 213134 - 223

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