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- PDB-8uhn: anti-Phosphohistidine Fab hSC44.ck.20.N32F with 3pHis peptide -

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Basic information

Entry
Database: PDB / ID: 8uhn
Titleanti-Phosphohistidine Fab hSC44.ck.20.N32F with 3pHis peptide
Components
  • (hSC44.ck.20.N32F Fab ...) x 2
  • 3pHis peptide
KeywordsIMMUNE SYSTEM / ANTI-PHOSPHOHISTIDINE ANTIBODY POST-TRANSLATIONAL MODIFICATION ANTIBODY HUMANIZATION
Function / homologyACETATE ION
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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) 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.N32F Fab heavy chain
L: hSC44.ck.20.N32F Fab light chain
A: hSC44.ck.20.N32F Fab heavy chain
B: hSC44.ck.20.N32F Fab light chain
C: 3pHis peptide
D: 3pHis peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,75710
Polymers96,5156
Non-polymers2424
Water5,675315
1
H: hSC44.ck.20.N32F Fab heavy chain
L: hSC44.ck.20.N32F Fab light chain
D: 3pHis peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3795
Polymers48,2583
Non-polymers1212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-29 kcal/mol
Surface area19330 Å2
MethodPISA
2
A: hSC44.ck.20.N32F Fab heavy chain
B: hSC44.ck.20.N32F Fab light chain
C: 3pHis peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3795
Polymers48,2583
Non-polymers1212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-30 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.280, 74.033, 239.278
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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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide 3pHis peptide


Mass: 747.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 2 types, 4 molecules HALB

#1: Antibody hSC44.ck.20.N32F Fab heavy chain


Mass: 23597.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody hSC44.ck.20.N32F Fab light chain


Mass: 23912.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 319 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08M sodium cacodylate, pH 6.5, 0.16M calcium acetate, 20% glycerol, 14.4% PEG-8000

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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: 2.09→47.19 Å / Num. obs: 71747 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 35.62 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Rrim(I) all: 0.11 / Rsym value: 0.101 / Χ2: 1.26 / Net I/σ(I): 16
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3417 / CC1/2: 0.4 / CC star: 0.756 / Rpim(I) all: 0.611 / Rrim(I) all: 1.44 / Rsym value: 1.3 / Χ2: 1.1 / % possible all: 92.7

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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: 2.09→47.19 Å / SU ML: 0.2917 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2446 3509 4.9 %
Rwork0.2175 68152 -
obs0.2188 71661 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.97 Å2
Refinement stepCycle: LAST / Resolution: 2.09→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6601 0 16 315 6932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00186760
X-RAY DIFFRACTIONf_angle_d0.51799181
X-RAY DIFFRACTIONf_chiral_restr0.04311031
X-RAY DIFFRACTIONf_plane_restr0.00321169
X-RAY DIFFRACTIONf_dihedral_angle_d12.87332377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.120.38511270.33812330X-RAY DIFFRACTION82.81
2.12-2.150.33071380.32232607X-RAY DIFFRACTION91.74
2.15-2.180.35651270.31022654X-RAY DIFFRACTION93.07
2.18-2.220.32471190.30742592X-RAY DIFFRACTION91.46
2.22-2.250.31931470.31182606X-RAY DIFFRACTION91.92
2.25-2.290.33241260.29882579X-RAY DIFFRACTION90.53
2.29-2.340.31311420.29792603X-RAY DIFFRACTION91.5
2.34-2.380.33811220.28852602X-RAY DIFFRACTION90.56
2.38-2.430.33471020.28082582X-RAY DIFFRACTION91.17
2.43-2.480.31091320.27632578X-RAY DIFFRACTION89.97
2.48-2.540.27491300.26432584X-RAY DIFFRACTION90.38
2.54-2.60.2871520.26682597X-RAY DIFFRACTION91.69
2.6-2.670.3071330.25762632X-RAY DIFFRACTION91.92
2.67-2.750.32391340.25692709X-RAY DIFFRACTION94.33
2.75-2.840.27421250.25162795X-RAY DIFFRACTION96.66
2.84-2.940.26131420.2462808X-RAY DIFFRACTION98.27
2.94-3.060.27471440.23372857X-RAY DIFFRACTION99.4
3.06-3.20.27921430.22492884X-RAY DIFFRACTION99.9
3.2-3.370.24291580.22182865X-RAY DIFFRACTION99.87
3.37-3.580.24071440.20732905X-RAY DIFFRACTION100
3.58-3.850.21521710.19472856X-RAY DIFFRACTION100
3.85-4.240.21790.16972901X-RAY DIFFRACTION100
4.24-4.850.16921640.14712921X-RAY DIFFRACTION100
4.86-6.120.18631510.16652986X-RAY DIFFRACTION100
6.12-47.190.23481570.19743119X-RAY DIFFRACTION99.94

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