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- PDB-8uht: anti-Phosphohistidine Fab hSC44.ck.20.elbow bound to Glu H1 -

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Basic information

Entry
Database: PDB / ID: 8uht
Titleanti-Phosphohistidine Fab hSC44.ck.20.elbow bound to Glu H1
Components
  • hSC44.ck.20.elbow Fab heavy chain
  • hSC44.ck.20.elbow Fab light chain
KeywordsIMMUNE SYSTEM / ANTI-PHOSPHOHISTIDINE ANTIBODY POST-TRANSLATIONAL MODIFICATION ANTIBODY HUMANIZATION
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 9, 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.20.elbow Fab heavy chain
L: hSC44.ck.20.elbow Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,5462
Polymers47,5462
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-23 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.745, 73.275, 148.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 23666.617 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.elbow 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris, pH 8.5, 8% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.45→47.17 Å / Num. obs: 19822 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 53.43 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Rsym value: 0.063 / Χ2: 1.19 / Net I/σ(I): 29.4
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.854 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 839 / CC1/2: 0.709 / CC star: 0.911 / Rpim(I) all: 0.387 / Rrim(I) all: 0.941 / Rsym value: 0.854 / Χ2: 1.15 / % possible all: 84.2

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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: 2.45→47.17 Å / SU ML: 0.4574 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2895 985 4.98 %
Rwork0.2441 18793 -
obs0.2465 19778 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.71 Å2
Refinement stepCycle: LAST / Resolution: 2.45→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 0 10 3287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493362
X-RAY DIFFRACTIONf_angle_d0.71184572
X-RAY DIFFRACTIONf_chiral_restr0.0465515
X-RAY DIFFRACTIONf_plane_restr0.0054584
X-RAY DIFFRACTIONf_dihedral_angle_d12.94731198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.580.45471160.36292344X-RAY DIFFRACTION85.89
2.58-2.750.41351320.36912544X-RAY DIFFRACTION92.21
2.75-2.960.47681330.34642691X-RAY DIFFRACTION97.82
2.96-3.250.35211250.31582754X-RAY DIFFRACTION99.21
3.26-3.730.32231490.28392746X-RAY DIFFRACTION99.14
3.73-4.690.28311690.20292774X-RAY DIFFRACTION99.43
4.69-47.170.19321610.17572940X-RAY DIFFRACTION99.42

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