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

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Basic information

Entry
Database: PDB / ID: 8uji
Titleanti-Phosphohistidine Fab hSC44.ck with 3pTza peptide
Components
  • 3-pTza 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: 1.95 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 11, 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
A: hSC44.CK Fab heavy chain
B: hSC44.CK Fab light chain
C: 3-pTza peptide
D: 3-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3237
Polymers96,2616
Non-polymers621
Water3,945219
1
H: hSC44.CK Fab heavy chain
L: hSC44.CK Fab light chain
D: 3-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1924
Polymers48,1303
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hSC44.CK Fab heavy chain
B: hSC44.CK Fab light chain
C: 3-pTza peptide


Theoretical massNumber of molelcules
Total (without water)48,1303
Polymers48,1303
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.498, 139.615, 73.616
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

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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
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): expi293F / 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
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): expi293F / Production host: Homo sapiens (human)
#3: Protein/peptide 3-pTza peptide


Mass: 748.641 Da / Num. of mol.: 2 / 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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Lithium 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: Jul 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→39.34 Å / Num. obs: 68051 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 29.81 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.044 / Rrim(I) all: 0.149 / Rsym value: 0.143 / Χ2: 1.35 / Net I/σ(I): 17.6
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.93 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3151 / CC1/2: 0.421 / CC star: 0.77 / Rpim(I) all: 0.673 / Rrim(I) all: 2.05 / Rsym value: 1.93 / Χ2: 1.04 / % possible all: 91.3

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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: 1.95→39.34 Å / SU ML: 0.2845 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2599 3393 4.99 %
Rwork0.2117 64623 -
obs0.2141 68016 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6600 0 4 219 6823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00566765
X-RAY DIFFRACTIONf_angle_d0.91429206
X-RAY DIFFRACTIONf_chiral_restr0.05261040
X-RAY DIFFRACTIONf_plane_restr0.00571174
X-RAY DIFFRACTIONf_dihedral_angle_d13.90922397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.39751100.34992274X-RAY DIFFRACTION82.95
1.98-2.010.40741250.322675X-RAY DIFFRACTION96.92
2.01-2.040.33261480.28652644X-RAY DIFFRACTION97.08
2.04-2.070.31921360.26742672X-RAY DIFFRACTION98.18
2.07-2.110.28131430.25712709X-RAY DIFFRACTION98.96
2.11-2.150.31571410.25852724X-RAY DIFFRACTION98.83
2.15-2.190.36681330.2632713X-RAY DIFFRACTION99.13
2.19-2.230.32161400.25282723X-RAY DIFFRACTION98.93
2.23-2.280.25871290.252687X-RAY DIFFRACTION98.5
2.28-2.340.33271430.25952703X-RAY DIFFRACTION98.89
2.34-2.40.29751320.24292735X-RAY DIFFRACTION99.07
2.4-2.460.32511530.24152672X-RAY DIFFRACTION97.35
2.46-2.530.3011420.24222535X-RAY DIFFRACTION92.02
2.53-2.610.2841440.23482707X-RAY DIFFRACTION98.79
2.61-2.710.29661480.23112723X-RAY DIFFRACTION99.24
2.71-2.820.26921560.22912738X-RAY DIFFRACTION99.04
2.82-2.940.24721440.23042734X-RAY DIFFRACTION98.83
2.94-3.10.28841670.22742730X-RAY DIFFRACTION98.74
3.1-3.290.27021530.21072701X-RAY DIFFRACTION98.14
3.29-3.550.26681370.20792711X-RAY DIFFRACTION97.3
3.55-3.90.27521370.20082628X-RAY DIFFRACTION93.41
3.9-4.470.20381440.16892801X-RAY DIFFRACTION99.53
4.47-5.630.18891600.1552831X-RAY DIFFRACTION99.2
5.63-39.340.18051280.1672853X-RAY DIFFRACTION94.94

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