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- PDB-8uit: anti-Phosphohistidine Fab hSC44.ck with 3pHis peptide -

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Basic information

Entry
Database: PDB / ID: 8uit
Titleanti-Phosphohistidine Fab hSC44.ck with 3pHis peptide
Components
  • 3pHis peptide
  • hSC44.ck Fab heavy chain
  • hSC44.ck Fab light chain
KeywordsIMMUNE SYSTEM / ANTI-PHOSPHOHISTIDINE ANTIBODY POST-TRANSLATIONAL MODIFICATION ANTIBODY HUMANIZATION
Biological speciesOryctolagus cuniculus (rabbit)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKalagiri, R. / Stanfield, R.L. / Hunter, T. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA242443 United States
CitationJournal: Biorxiv / Year: 2024
Title: Using phage display for rational engineering of a higher affinity humanized 3' phosphohistidine-specific antibody.
Authors: Martyn, G.D. / Kalagiri, R. / Veggiani, G. / Stanfield, R.L. / Choudhuri, I. / Sala, M. / Meisenhelder, J. / Chen, C. / Biswas, A. / Levy, R.M. / Lyumkis, D. / Wilson, I.A. / Hunter, T. / Sidhu, S.S.
History
DepositionOct 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 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: hSC44.ck Fab heavy chain
L: hSC44.ck Fab light chain
B: hSC44.ck Fab light chain
A: hSC44.ck Fab heavy chain
C: 3pHis peptide
D: 3pHis peptide


Theoretical massNumber of molelcules
Total (without water)96,2596
Polymers96,2596
Non-polymers00
Water1,13563
1
H: hSC44.ck Fab heavy chain
L: hSC44.ck Fab light chain
C: 3pHis peptide


Theoretical massNumber of molelcules
Total (without water)48,1293
Polymers48,1293
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hSC44.ck Fab light chain
A: hSC44.ck Fab heavy chain
D: 3pHis peptide


Theoretical massNumber of molelcules
Total (without water)48,1293
Polymers48,1293
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.247, 139.056, 73.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11H-317-

HOH

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Components

#1: Antibody hSC44.ck Fab heavy chain


Mass: 23502.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fab heavy chain / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody hSC44.ck Fab light chain


Mass: 23879.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fab light chain / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Protein/peptide 3pHis peptide


Mass: 747.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Calcium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→39.72 Å / Num. obs: 49506 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 41.37 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.064 / Rrim(I) all: 0.23 / Rsym value: 0.221 / Χ2: 1.2 / Net I/σ(I): 17.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9.4 % / Rmerge(I) obs: 4.8 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2432 / CC1/2: 0.5 / CC star: 0.82 / Rpim(I) all: 1.66 / Rrim(I) all: 5.1 / Rsym value: 4.8 / Χ2: 0.89 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.72 Å / SU ML: 0.314 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.5231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 2489 5.04 %
Rwork0.2301 46925 -
obs0.2323 49414 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.62 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 0 63 6668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00246776
X-RAY DIFFRACTIONf_angle_d0.60449224
X-RAY DIFFRACTIONf_chiral_restr0.04291042
X-RAY DIFFRACTIONf_plane_restr0.00421177
X-RAY DIFFRACTIONf_dihedral_angle_d12.21952400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.37281350.39122452X-RAY DIFFRACTION93.83
2.24-2.280.36671270.35722556X-RAY DIFFRACTION99.78
2.28-2.330.38181300.33512589X-RAY DIFFRACTION99.89
2.33-2.390.42981300.31522591X-RAY DIFFRACTION99.89
2.39-2.450.35661540.30732558X-RAY DIFFRACTION99.93
2.45-2.510.35471270.30292587X-RAY DIFFRACTION99.89
2.51-2.590.3251310.29342611X-RAY DIFFRACTION99.96
2.59-2.670.33811230.28672605X-RAY DIFFRACTION99.82
2.67-2.770.34581290.27292606X-RAY DIFFRACTION99.85
2.77-2.880.3461470.2722546X-RAY DIFFRACTION99.89
2.88-3.010.29351180.2812640X-RAY DIFFRACTION99.82
3.01-3.170.37871540.27292601X-RAY DIFFRACTION99.96
3.17-3.370.28631530.24582597X-RAY DIFFRACTION99.93
3.37-3.630.28411440.2342614X-RAY DIFFRACTION99.82
3.63-3.990.26211520.21422625X-RAY DIFFRACTION99.68
3.99-4.570.20791350.16952662X-RAY DIFFRACTION99.86
4.57-5.750.19031450.16132680X-RAY DIFFRACTION99.93
5.75-38.720.21741550.18232805X-RAY DIFFRACTION99.7

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