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- PDB-3umt: scFv12, Anti-BclA antibody single chain variable fragment -

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Basic information

Entry
Database: PDB / ID: 3umt
TitlescFv12, Anti-BclA antibody single chain variable fragment
ComponentsscFv heavy chain and light chain
KeywordsIMMUNE SYSTEM / scFv / stability engineering / Anthrax / Anti-BclA antibody / Immunoglobulin fold (VH and VL domains) / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsPokkuluri, P.R.
CitationJournal: To be Published
Title: Systematic stability engineering of single-chain antibodies
Authors: Wilton, R. / Londer, Y.Y. / Hanson, D.K. / Zerbs, S. / Dirks, A. / Warner, C. / Carney, J.P. / Pokkuluri, P.R. / Stevens, F.J.
History
DepositionNov 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: scFv heavy chain and light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6562
Polymers27,4481
Non-polymers2071
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.290, 65.290, 96.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21A-352-

HOH

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Components

#1: Antibody scFv heavy chain and light chain


Mass: 27448.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PROTEIN CRYSTALLIZED IS A SINGLE CHAIN ANTIBODY FRAGMENT
Has protein modificationY
Sequence detailsRESIDUES 3-121 CORRESPONDS TO VH DOMAIN AND RESIDUES 138-248 CORRESPOND TO THE VL DOMAIN. THE ...RESIDUES 3-121 CORRESPONDS TO VH DOMAIN AND RESIDUES 138-248 CORRESPOND TO THE VL DOMAIN. THE LINKER SEQUENCE IS GGGGSGGGGSGGGGST

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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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1M Sodium citrate, 0.1 M CHES pH9.5 diluted by water 4:1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.798→100 Å / Num. all: 22646 / Num. obs: 22608 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 60
Reflection shellResolution: 1.798→1.83 Å / Redundancy: 12 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1095 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VH domain from structure 1KTR, VL domain from structure 1FGV

1ktr

1fgv


Resolution: 1.798→30.914 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1153 5.12 %random
Rwork0.1748 ---
obs0.1772 22528 99.65 %-
all-22608 --
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.358 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1573 Å20 Å20 Å2
2--0.1573 Å2-0 Å2
3----0.3146 Å2
Refinement stepCycle: LAST / Resolution: 1.798→30.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 13 203 1940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161776
X-RAY DIFFRACTIONf_angle_d1.6272406
X-RAY DIFFRACTIONf_dihedral_angle_d16.917638
X-RAY DIFFRACTIONf_chiral_restr0.118267
X-RAY DIFFRACTIONf_plane_restr0.009302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.88030.22951610.18192609X-RAY DIFFRACTION100
1.8803-1.97940.21231320.18332653X-RAY DIFFRACTION100
1.9794-2.10340.23291440.18082643X-RAY DIFFRACTION100
2.1034-2.26580.23991390.17292641X-RAY DIFFRACTION100
2.2658-2.49370.2311540.18932643X-RAY DIFFRACTION100
2.4937-2.85430.23361390.18552675X-RAY DIFFRACTION99
2.8543-3.59530.23451300.17152694X-RAY DIFFRACTION99
3.5953-30.91820.20431540.16572817X-RAY DIFFRACTION99

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