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- PDB-5obf: fAb. AbVance: increasing our knowledge of antibody structural spa... -

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Basic information

Entry
Database: PDB / ID: 5obf
TitlefAb. AbVance: increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery.
Components
  • fAb Heavy chainFragment antigen-binding
  • fAb Light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / fAb / AbVance project / Pistoia Alliance
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.92 Å
AuthorsVicentini, G. / Convery, M.A.
CitationJournal: To Be Published
Title: AbVance: increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery
Authors: Convery, M.A.
History
DepositionJun 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: fAb Heavy chain
L: fAb Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4565
Polymers47,1752
Non-polymers2803
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-26 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.397, 132.397, 56.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11H-508-

HOH

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Components

#1: Antibody fAb Heavy chain / Fragment antigen-binding


Mass: 23135.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody fAb Light chain / Fragment antigen-binding


Mass: 24039.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 550 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M Tris pH8.5 2M Ammonium Sulfate 15% glycerol used as cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.91→27.96 Å / Num. obs: 37566 / % possible obs: 97.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 28.62 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 20.1
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4686 / % possible all: 83.8

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 1.92→21.49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1881 5.01 %RANDOM
Rwork0.174 ---
obs0.175 37548 99.4 %-
Displacement parametersBiso mean: 38.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.0732 Å20 Å20 Å2
2---0.0732 Å20 Å2
3---0.1465 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.92→21.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 17 550 3848
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013408HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094655HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1123SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes491HARMONIC5
X-RAY DIFFRACTIONt_it3408HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion15.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion465SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4240SEMIHARMONIC4
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.253 133 5.01 %
Rwork0.205 2522 -
all0.207 2655 -
obs--92.31 %
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)
13.203-0.39620.32731.3844-0.7480.9128-0.0147-0.0625-0.2633-0.0895-0.1191-0.09210.07320.06990.1338-0.15250.02230.0519-0.10740.0074-0.08590.0826.15561.6351
22.432-0.13350.45040.4898-0.07220.257-0.01260.06080.36390.0560.05560.0779-0.0744-0.1173-0.043-0.09020.02530.0418-0.03590.0406-0.03649.760239.5173-5.8435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ H|* }
2X-RAY DIFFRACTION2{ L|* }

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