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- PDB-4b41: Crystal structure of an amyloid-beta binding single chain antibody G7 -

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Basic information

Entry
Database: PDB / ID: 4b41
TitleCrystal structure of an amyloid-beta binding single chain antibody G7
ComponentsANTIBODY G7
KeywordsIMMUNE SYSTEM / ALZHEIMER'S DISEASE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.191 Å
AuthorsBeringer, D.X. / Dorresteijn, B. / Rutten, L. / Wienk, H. / el Khattabi, M. / Kroon-Batenburg, L.M.J. / Verrips, C.T.
CitationJournal: To be Published
Title: Crystal Structure of an Amyloid-Beta Binding Single Chain Antibody G7
Authors: Beringer, D.X. / Dorresteijn, B. / Rutten, L. / Wienk, H. / El Khattabi, M. / Kroon-Batenburg, L.M.J. / Verrips, C.T.
History
DepositionJul 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIBODY G7
B: ANTIBODY G7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5687
Polymers25,3342
Non-polymers2345
Water5,296294
1
A: ANTIBODY G7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7383
Polymers12,6671
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANTIBODY G7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8304
Polymers12,6671
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.178, 32.596, 52.197
Angle α, β, γ (deg.)103.74, 99.54, 90.62
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody ANTIBODY G7


Mass: 12667.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMEK220 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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: 1.75 Å3/Da / Density % sol: 29.6 % / Description: NONE
Crystal growpH: 5.2 / Details: 0.1 M NA CITRATE PH 5.2, 0.2 NACL, 26-30% PEG8K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2010 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→49.94 Å / Num. obs: 50156 / % possible obs: 85.1 % / Observed criterion σ(I): 6.7 / Redundancy: 3.4 % / Biso Wilson estimate: 10.26 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.6
Reflection shellResolution: 1.19→1.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 6.7 / % possible all: 62.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EZJ

3ezj


Resolution: 1.191→49.936 Å / SU ML: 0.09 / σ(F): 1.96 / Phase error: 18.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1619 2546 5.1 %
Rwork0.136 --
obs0.1374 50144 85.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 1.191→49.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 10 294 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061996
X-RAY DIFFRACTIONf_angle_d1.1322721
X-RAY DIFFRACTIONf_dihedral_angle_d10.743747
X-RAY DIFFRACTIONf_chiral_restr0.075294
X-RAY DIFFRACTIONf_plane_restr0.004365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1911-1.2140.1876620.1461145X-RAY DIFFRACTION36
1.214-1.23870.17141230.13322387X-RAY DIFFRACTION78
1.2387-1.26570.14521350.1282553X-RAY DIFFRACTION82
1.2657-1.29510.17931160.1272566X-RAY DIFFRACTION82
1.2951-1.32750.18951460.13352628X-RAY DIFFRACTION83
1.3275-1.36340.16631330.13622597X-RAY DIFFRACTION84
1.3634-1.40350.17061280.13092608X-RAY DIFFRACTION84
1.4035-1.44880.2021480.13292710X-RAY DIFFRACTION88
1.4488-1.50060.17321240.1342778X-RAY DIFFRACTION88
1.5006-1.56070.17041400.13582828X-RAY DIFFRACTION90
1.5607-1.63170.18351480.12742854X-RAY DIFFRACTION91
1.6317-1.71780.17041550.12942824X-RAY DIFFRACTION92
1.7178-1.82540.17861570.13292861X-RAY DIFFRACTION92
1.8254-1.96640.15921790.12772758X-RAY DIFFRACTION91
1.9664-2.16420.15341730.12352853X-RAY DIFFRACTION92
2.1642-2.47740.15271570.13852846X-RAY DIFFRACTION92
2.4774-3.12120.18081670.15082868X-RAY DIFFRACTION93
3.1212-49.97960.13821550.14042934X-RAY DIFFRACTION94

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