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- PDB-8uhh: anti-Phosphohistidine Fab hSC44.ck.elbow.20.N32F -

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Basic information

Entry
Database: PDB / ID: 8uhh
Titleanti-Phosphohistidine Fab hSC44.ck.elbow.20.N32F
Components(hSC44.ck.elbow.20.N32F Fab ...) x 2
KeywordsIMMUNE SYSTEM / ANTI-PHOSPHOHISTIDINE ANTIBODY POST-TRANSLATIONAL MODIFICATION ANTIBODY HUMANIZATION
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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.elbow.20.N32F Fab heavy chain
L: hSC44.ck.elbow.20.N32F Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9506
Polymers47,5792
Non-polymers3714
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-32 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.574, 72.072, 152.189
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

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Antibody , 2 types, 2 molecules HL

#1: Antibody hSC44.ck.elbow.20.N32F 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.elbow.20.N32F Fab light chain


Mass: 23912.453 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)

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Non-polymers , 4 types, 463 molecules

#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, pH 7.5, 20% PEG4000, 10% 2-propanol

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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: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.84→46.27 Å / Num. obs: 46607 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 25.39 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Rsym value: 0.1 / Χ2: 1.4 / Net I/σ(I): 21
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.78 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 2191 / CC1/2: 0.371 / CC star: 0.736 / Rpim(I) all: 0.904 / Rrim(I) all: 2 / Rsym value: 1.78 / Χ2: 1.2 / % possible all: 94.4

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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: 1.84→46.27 Å / SU ML: 0.2366 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 2299 4.94 %
Rwork0.2039 44224 -
obs0.2055 46523 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.74 Å2
Refinement stepCycle: LAST / Resolution: 1.84→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 21 459 3785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543436
X-RAY DIFFRACTIONf_angle_d0.86084677
X-RAY DIFFRACTIONf_chiral_restr0.05526
X-RAY DIFFRACTIONf_plane_restr0.0073594
X-RAY DIFFRACTIONf_dihedral_angle_d13.91381238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.34991280.37682437X-RAY DIFFRACTION88.33
1.88-1.930.27341360.30332629X-RAY DIFFRACTION95.58
1.93-1.970.33581410.27832695X-RAY DIFFRACTION97.66
1.97-2.030.32151490.26772747X-RAY DIFFRACTION98.81
2.03-2.090.27861280.25122731X-RAY DIFFRACTION99.79
2.09-2.150.25831460.23382758X-RAY DIFFRACTION99.93
2.15-2.230.28521410.22422781X-RAY DIFFRACTION99.97
2.23-2.320.29171630.22262756X-RAY DIFFRACTION100
2.32-2.430.24361450.21282791X-RAY DIFFRACTION100
2.43-2.550.26831470.20672769X-RAY DIFFRACTION100
2.55-2.710.2351380.20422803X-RAY DIFFRACTION100
2.72-2.920.23871420.2042790X-RAY DIFFRACTION100
2.92-3.220.22581370.18952826X-RAY DIFFRACTION100
3.22-3.680.25521580.18372817X-RAY DIFFRACTION100
3.68-4.640.16281620.15432860X-RAY DIFFRACTION100
4.64-46.270.2091380.19663034X-RAY DIFFRACTION99.97

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