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- PDB-9mfn: Crystal Structure of ADI-64596 (human Fab, with substituted IgG1-... -

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Basic information

Entry
Database: PDB / ID: 9mfn
TitleCrystal Structure of ADI-64596 (human Fab, with substituted IgG1-CH1 (HC-L145Q, K147E, and S181E) and substituted kappa constant domain (LC-T129R, T178R, and T180Q))
Components
  • ADI-64596 Fab heavy chain
  • ADI-64596 Fab light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homologyBROMIDE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBattles, M.B. / Welin, M. / Laursen, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Mabs / Year: 2025
Title: Design of orthogonal constant domain interfaces to aid proper heavy/light chain pairing of bispecific antibodies.
Authors: Barlow, K.A. / Battles, M.B. / Brown, M.E. / Canfield, K. / Lu, X. / Lynaugh, H. / Morrill, M. / Rappazzo, C.G. / Reyes, S.P. / Sandberg, C. / Sharkey, B. / Strong, C. / Zhao, J. / Sivasubramanian, A.
History
DepositionDec 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: ADI-64596 Fab heavy chain
L: ADI-64596 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5447
Polymers47,0922
Non-polymers4525
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-12 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.594, 65.594, 96.795
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody ADI-64596 Fab heavy chain


Mass: 23573.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: substituted IgG1-CH1 (HC-L145Q, K147E, and S181E / Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody ADI-64596 Fab light chain


Mass: 23519.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: substituted kappa constant domain (LC-T129R, T178R, and T180Q
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.55 Å3/Da / Density % sol: 51.82 % / Description: needle-like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ADI-64596 (human Fab) was received at a concentration of 11.35 mg/mL in a buffer containing 2 mM Tris-HCl pH 8.0 and 150 mM NaCl. The PACT, BCS, and JCSG+ screens (all from Molecular ...Details: ADI-64596 (human Fab) was received at a concentration of 11.35 mg/mL in a buffer containing 2 mM Tris-HCl pH 8.0 and 150 mM NaCl. The PACT, BCS, and JCSG+ screens (all from Molecular Dimensions Ltd.) were initially set up using a mosquito crystallization robot (STP Labtech). Since crystals obtained from these initial screens only gave rise to low-resolution X-ray diffraction, crystal seed solutions were prepared and applied in the setup of the BCS, PACT, and Additive Screens (Hampton Research). Sitting drops of 160 nL protein and 160 nL precipitant solution were left to equilibrate against a 40 uL reservoir at 20 degrees C. After a few days, plate- and needle-like crystals appeared in several conditions. The precipitant solution giving rise to the best-diffracting crystal contained 75 mM Tris pH 8.5, 25 mM Bis-Tris-propane pH 8.5, 22.5% (v/v) PEG Smear Low, 5% (w/v) PEG3350, and 50 mM NaBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→96.79 Å / Num. obs: 208056 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.997 / Net I/σ(I): 7.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 19723 / CC1/2: 0.537 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→48.99 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 879 4.53 %
Rwork0.2083 --
obs0.2089 19398 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 17 38 3292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023347
X-RAY DIFFRACTIONf_angle_d0.5514558
X-RAY DIFFRACTIONf_dihedral_angle_d12.5041207
X-RAY DIFFRACTIONf_chiral_restr0.044517
X-RAY DIFFRACTIONf_plane_restr0.004585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.50.37641340.33173090X-RAY DIFFRACTION100
2.5-2.690.33051440.30973076X-RAY DIFFRACTION100
2.69-2.960.40121080.26313146X-RAY DIFFRACTION100
2.96-3.390.29781410.26553093X-RAY DIFFRACTION100
3.39-4.260.22121560.19093065X-RAY DIFFRACTION100
4.27-48.990.15281960.14723049X-RAY DIFFRACTION100
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)
16.0298-1.7868-3.0483.54332.72392.7658-0.6648-0.22290.95160.2017-0.36520.1453-0.0823-1.24030.84530.39180.0819-0.11610.7217-0.2260.7282.6643-7.2653-9.416
23.7897-4.65743.08687.9902-1.14385.7720.0357-0.11162.3248-0.2036-1.1822-0.8011-0.9174-0.39880.33650.48540.0512-0.19380.4876-0.18031.046911.2684-1.5554-4.6267
31.2396-0.41461.3970.7596-0.1581.7632-0.7306-0.45361.1663-0.024-0.6577-0.1362-0.9135-0.64370.03340.87210.3846-0.57960.6497-0.31571.83484.79325.6356-7.9006
45.3941-0.62690.8773.22920.9384.7705-0.6112-0.33621.89260.1826-0.08750.066-0.1913-0.85730.45250.4140.0801-0.11340.5811-0.15010.80077.3038-4.9995-6.369
54.5692-1.96131.6185.5582-2.32714.91010.65040.6011-0.5477-0.775-0.07970.05811.0019-0.1071-0.58410.5542-0.0433-0.18760.65650.14050.396416.3018-28.6158-19.5502
63.8495-0.37320.33454.4175-0.67053.4220.4045-0.1444-0.50710.40450.08920.21760.7817-0.4787-0.42750.6107-0.0826-0.12360.57910.22590.414816.4055-31.5727-11.4675
76.4416-2.36231.76243.1179-4.07025.85820.5204-0.3877-1.3534-0.26110.42611.45640.9459-0.9512-0.8270.6075-0.1764-0.16950.69930.23940.61178.8631-32.6765-16.0648
81.02420.3065-0.19530.40860.66021.3229-0.6987-1.00422.02760.8019-0.2635-0.9861-0.59320.3903-0.65530.69330.27-0.55770.6595-0.72521.415125.3814-3.67147.8748
91.2240.36580.28130.82950.3743.0707-0.6873-1.2621.86090.49930.5879-0.34090.0293-0.53440.28180.68990.3687-0.34180.7239-0.59731.049519.185-7.1389.487
108.8522-2.1665-2.96396.60922.49141.51770.5464-0.48580.8351-0.6563-0.08880.06480.47170.3210.75340.75870.3265-0.41990.637-0.22150.28931.5017-24.2534.6763
111.7551-0.7004-1.06093.34971.74036.05650.150.2017-0.06140.05440.2631-0.09130.8343-0.1032-0.39950.66580.1021-0.25040.450.01120.410228.9853-34.3464-14.4489
124.42670.0313-2.53864.71713.32673.839-0.0842-0.35850.05480.33080.7142-0.69931.02010.966-0.73870.53080.1174-0.13150.6209-0.06140.505236.063-30.6369-19.3957
131.9955-0.6046-0.24840.9208-0.47323.76130.13850.13580.08590.13280.5483-0.16131.23680.1678-0.58970.74050.1267-0.30010.5434-0.06950.537631.937-35.5453-13.7535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 33 )
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 53 )
3X-RAY DIFFRACTION3chain 'H' and (resid 54 through 74 )
4X-RAY DIFFRACTION4chain 'H' and (resid 75 through 115 )
5X-RAY DIFFRACTION5chain 'H' and (resid 116 through 151 )
6X-RAY DIFFRACTION6chain 'H' and (resid 152 through 199 )
7X-RAY DIFFRACTION7chain 'H' and (resid 200 through 219 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 38 )
9X-RAY DIFFRACTION9chain 'L' and (resid 39 through 101 )
10X-RAY DIFFRACTION10chain 'L' and (resid 102 through 113 )
11X-RAY DIFFRACTION11chain 'L' and (resid 114 through 150 )
12X-RAY DIFFRACTION12chain 'L' and (resid 151 through 163 )
13X-RAY DIFFRACTION13chain 'L' and (resid 164 through 213 )

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