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- PDB-4gqp: Structure based design of sub-nanomolar affinity anti-methampheta... -

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Basic information

Entry
Database: PDB / ID: 4gqp
TitleStructure based design of sub-nanomolar affinity anti-methamphetamine single chain antibodies.
ComponentsAnti-METH scFv
KeywordsIMMUNE SYSTEM / Antibody METH complex / Immunoglobulin fold / anti-METH single chain antibody / free METH concentration / Methamphetamine / vasculature
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2S)-N-methyl-1-phenylpropan-2-amine
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThakkar, S. / Varughese, K.I.
CitationJournal: Sci Rep / Year: 2014
Title: Affinity improvement of a therapeutic antibody to methamphetamine and amphetamine through structure-based antibody engineering.
Authors: Thakkar, S. / Nanaware-Kharade, N. / Celikel, R. / Peterson, E.C. / Varughese, K.I.
History
DepositionAug 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2May 2, 2018Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
H: Anti-METH scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9562
Polymers26,8061
Non-polymers1491
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.516, 65.265, 48.483
Angle α, β, γ (deg.)90.00, 98.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Anti-METH scFv


Mass: 26806.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: both heavy and light chains are attached to each other by a polypeptide linker
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pPICZ alpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33
#2: Chemical ChemComp-B40 / (2S)-N-methyl-1-phenylpropan-2-amine / Methamphetamine


Mass: 149.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE NUMBERS FOR THIS ENTRY FOLLOW THE KABAT NUMBERING SCHEME. NUMBERING 1-112 CORRESPONDS ...THE SEQUENCE NUMBERS FOR THIS ENTRY FOLLOW THE KABAT NUMBERING SCHEME. NUMBERING 1-112 CORRESPONDS TO THE HEAVY CHAIN AND 1001-1112 TO THE LIGHT CHAIN.

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 0.917 M sodium citrate, pH 8.2, 0.324 M imidazole-malate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 25, 2012 / Details: Rh coated flat mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 14299 / Num. obs: 14299 / % possible obs: 99.2 % / Redundancy: 4.8 % / Rsym value: 0.087 / Net I/σ(I): 34.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 8.1 / Rsym value: 0.33 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.5.0109refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GKZ

3gkz


Resolution: 2→38.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.145 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25361 719 5 %RANDOM
Rwork0.19369 ---
obs0.19669 13554 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.454 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 11 79 1846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221812
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.9512440
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4615216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73723.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95715283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.744155
X-RAY DIFFRACTIONr_chiral_restr0.1350.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211321
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.211.51134
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.03921809
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1483678
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.364.5631
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 58 -
Rwork0.196 997 -
obs--99.15 %
Refinement TLS params.Method: refined / Origin x: 3.5851 Å / Origin y: -2.2075 Å / Origin z: 13.6952 Å
111213212223313233
T0.0156 Å20.0018 Å20.0052 Å2-0.0525 Å20.0061 Å2--0.0524 Å2
L0.1209 °20.1728 °20.0889 °2-1.5502 °2-0.4444 °2--0.319 °2
S0.0162 Å °-0.0013 Å °-0.0087 Å °0.0795 Å °-0.0303 Å °-0.0611 Å °-0.0224 Å °0.005 Å °0.0141 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 1106
2X-RAY DIFFRACTION1H1201
3X-RAY DIFFRACTION1H1301 - 1379

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