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- PDB-8uih: anti-Phosphohistidine Fab hSC44.ck.20 with 3pTza peptide -

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Basic information

Entry
Database: PDB / ID: 8uih
Titleanti-Phosphohistidine Fab hSC44.ck.20 with 3pTza peptide
Components
  • 3ptza peptide
  • hSC44.ck.20 Fab heavy chain
  • hSC44.ck.20 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: 1.85 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

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Assembly

Deposited unit
H: hSC44.ck.20 Fab heavy chain
L: hSC44.ck.20 Fab light chain
D: 3ptza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3505
Polymers48,2253
Non-polymers1242
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.958, 73.115, 88.071
Angle α, β, γ (deg.)90.000, 111.244, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody hSC44.ck.20 Fab heavy chain


Mass: 23597.467 Da / Num. of mol.: 1
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.20 Fab light chain


Mass: 23879.383 Da / Num. of mol.: 1
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 3ptza peptide


Mass: 748.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M tri-potassium citrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.85→41.04 Å / Num. obs: 40163 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 22.27 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.074 / Rrim(I) all: 0.151 / Rsym value: 0.131 / Χ2: 1.001 / Net I/σ(I): 9.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 1984 / CC1/2: 0.362 / CC star: 0.729 / Rpim(I) all: 0.79 / Rrim(I) all: 1.51 / Rsym value: 1.28 / Χ2: 0.96 / % possible all: 99.4

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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: 1.85→41.04 Å / SU ML: 0.2842 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2434 1978 4.93 %
Rwork0.205 38174 -
obs0.2069 40152 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.97 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 8 263 3592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323420
X-RAY DIFFRACTIONf_angle_d0.74614652
X-RAY DIFFRACTIONf_chiral_restr0.0471525
X-RAY DIFFRACTIONf_plane_restr0.0041593
X-RAY DIFFRACTIONf_dihedral_angle_d12.25071213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.42071380.38192482X-RAY DIFFRACTION92.29
1.9-1.950.32331500.32632725X-RAY DIFFRACTION99.58
1.95-20.29831610.28992765X-RAY DIFFRACTION99.86
2-2.070.29791320.25372669X-RAY DIFFRACTION99.54
2.07-2.140.31121330.24922750X-RAY DIFFRACTION99.65
2.14-2.230.27741210.23442728X-RAY DIFFRACTION99.69
2.23-2.330.28781330.24762754X-RAY DIFFRACTION99.76
2.33-2.450.23891350.21352771X-RAY DIFFRACTION100
2.45-2.610.26771350.2162731X-RAY DIFFRACTION99.97
2.61-2.810.24491320.21092755X-RAY DIFFRACTION99.86
2.81-3.090.24281430.20972740X-RAY DIFFRACTION99.93
3.09-3.540.24911730.18282720X-RAY DIFFRACTION99.93
3.54-4.460.20671360.15032785X-RAY DIFFRACTION99.93
4.46-41.040.16861560.15982799X-RAY DIFFRACTION99.8

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