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- PDB-3dv4: Crystal structure of SAG506-01, tetragonal, crystal 1 -

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Basic information

Entry
Database: PDB / ID: 3dv4
TitleCrystal structure of SAG506-01, tetragonal, crystal 1
Components
  • Ig-like protein
  • antibody Fv fragment SAG506-01
KeywordsIMMUNE SYSTEM / antibody / KDO / twinning / pseudo-symmetry
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / Vk protein / VH coding region
Similarity search - Component
Biological speciesMus Musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsBrooks, C.L. / Blackler, R.J. / Gerstenbruch, S. / Kosma, P. / Muller-Loennies, S. / Brade, H. / Evans, S.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Pseudo-symmetry and twinning in crystals of homologous antibody Fv fragments.
Authors: Brooks, C.L. / Blackler, R.J. / Gerstenbruch, S. / Kosma, P. / Muller-Loennies, S. / Brade, H. / Evans, S.V.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antibody Fv fragment SAG506-01
B: Ig-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2545
Polymers25,7972
Non-polymers4573
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-12 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.510, 72.510, 85.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-153-

HOH

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody antibody Fv fragment SAG506-01


Mass: 12353.851 Da / Num. of mol.: 1 / Fragment: variable region fragment (Fv)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus Musculus (house mouse) / Plasmid: pSFJ8 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: A0N262*PLUS
#2: Antibody Ig-like protein


Mass: 13442.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus Musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: A2NU21*PLUS

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid


Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H14O8
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 133 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: PEG 4000, MgCl2, pH 8.5, vapor diffusion, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→19.81 Å / Num. obs: 17255 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.07 / Χ2: 1 / Net I/σ(I): 14.7 / Scaling rejects: 1226
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.95-2.029.110.4254.41540516861.1999.8
2.02-2.19.220.3754.91565216911.19100
2.1-2.29.450.3025.81610616971.16100
2.2-2.319.530.266.71621216931.1100
2.31-2.469.60.2177.91638616991.0899.9
2.46-2.659.680.1679.71659917041100
2.65-2.919.650.10813.71684417350.9100
2.91-3.339.650.06520.71691217430.82100
3.33-4.199.540.04230.51686017520.7699.9
4.19-19.818.630.03441.61645018550.8399.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.54 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.81 Å
Translation2.5 Å19.81 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.81 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.68 / SU ML: 0.44 / σ(F): 1.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.336 872 5.06 %
Rwork0.269 --
obs0.272 17229 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.158 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 66.35 Å2 / Biso mean: 37.986 Å2 / Biso min: 19.22 Å2
Baniso -1Baniso -2Baniso -3
1-8.9 Å20 Å2-0 Å2
2--8.9 Å2-0 Å2
3----17.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 30 131 1955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031862
X-RAY DIFFRACTIONf_angle_d0.6142511
X-RAY DIFFRACTIONf_chiral_restr0.041271
X-RAY DIFFRACTIONf_plane_restr0.002314
X-RAY DIFFRACTIONf_dihedral_angle_d16.049661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.0720.4141470.39126672814100
2.072-2.2320.4271480.3426612809100
2.232-2.4560.3751410.32526832824100
2.456-2.8110.391570.30727062863100
2.811-3.5380.3141500.26127392889100
3.538-19.8110.2721290.2152901303099

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