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- PDB-8uig: anti-Phosphohistidine Fab hSC44.ck.20 with 3pHis peptide -

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Basic information

Entry
Database: PDB / ID: 8uig
Titleanti-Phosphohistidine Fab hSC44.ck.20 with 3pHis peptide
Components
  • 3pHis 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: 1.9 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
C: 3pHis peptide


Theoretical massNumber of molelcules
Total (without water)48,2253
Polymers48,2253
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-31 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.111, 72.605, 70.325
Angle α, β, γ (deg.)90.000, 98.207, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,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 3pHis peptide


Mass: 747.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M tri-potassium citrate, 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: 1.9→34.82 Å / Num. obs: 33299 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 20.88 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.082 / Rrim(I) all: 0.183 / Rsym value: 0.162 / Χ2: 1.46 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1333 / CC1/2: 0.33 / CC star: 0.705 / Rpim(I) all: 0.719 / Rrim(I) all: 1.41 / Rsym value: 1.2 / Χ2: 1.065 / % possible all: 77.1

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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: 1.9→34.82 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2132 1721 5.17 %
Rwork0.1722 31562 -
obs0.1742 33283 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 187 3512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00453409
X-RAY DIFFRACTIONf_angle_d0.76934637
X-RAY DIFFRACTIONf_chiral_restr0.049522
X-RAY DIFFRACTIONf_plane_restr0.0046592
X-RAY DIFFRACTIONf_dihedral_angle_d14.28761204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.27911120.23892116X-RAY DIFFRACTION77.63
1.96-2.020.26651310.21952611X-RAY DIFFRACTION95.14
2.02-2.090.23011290.2022693X-RAY DIFFRACTION98.22
2.09-2.180.22361350.18342689X-RAY DIFFRACTION98.12
2.18-2.270.25281830.18392649X-RAY DIFFRACTION98.4
2.27-2.390.21081540.18092660X-RAY DIFFRACTION98.63
2.39-2.540.22481510.18422603X-RAY DIFFRACTION94.97
2.54-2.740.21891700.18752702X-RAY DIFFRACTION98.69
2.74-3.020.24481300.18062711X-RAY DIFFRACTION98.82
3.02-3.450.22941310.18212726X-RAY DIFFRACTION98.48
3.45-4.350.16331530.14322644X-RAY DIFFRACTION96.18
4.35-34.820.18531420.14022758X-RAY DIFFRACTION97.84

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