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- PDB-8uio: anti-Phosphohistidine Fab hSC44.ck -

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Basic information

Entry
Database: PDB / ID: 8uio
Titleanti-Phosphohistidine Fab hSC44.ck
Components
  • hSC44.ck Fab heavy chain
  • hSC44.ck Fab light chain
KeywordsIMMUNE SYSTEM / ANTI-PHOSPHOHISTIDINE ANTIBODY POST-TRANSLATIONAL MODIFICATION ANTIBODY HUMANIZATION
Function / homologyCITRIC ACID
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1486
Polymers94,7634
Non-polymers3842
Water7,927440
1
H: hSC44.ck Fab heavy chain
L: hSC44.ck Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5743
Polymers47,3822
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-20 kcal/mol
Surface area19490 Å2
MethodPISA
2
A: hSC44.ck Fab heavy chain
B: hSC44.ck Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5743
Polymers47,3822
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-21 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.818, 138.848, 73.214
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
Details: Fab heavy chain / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / 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
Details: Fab light chain / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.11 %
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: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.75→46.91 Å / Num. obs: 95210 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 22.45 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.049 / Rrim(I) all: 0.133 / Rsym value: 0.124 / Χ2: 1.35 / Net I/σ(I): 16.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 4089 / CC1/2: 0.38 / CC star: 0.74 / Rpim(I) all: 0.53 / Rrim(I) all: 1.29 / Rsym value: 1.17 / % possible all: 85.3

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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: 1.75→46.91 Å / SU ML: 0.2184 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 4802 5.05 %
Rwork0.2104 90339 -
obs0.2118 95141 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 26 440 6977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00566708
X-RAY DIFFRACTIONf_angle_d0.83029135
X-RAY DIFFRACTIONf_chiral_restr0.05251032
X-RAY DIFFRACTIONf_plane_restr0.0061169
X-RAY DIFFRACTIONf_dihedral_angle_d14.26532389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.40741350.34312476X-RAY DIFFRACTION81.95
1.77-1.790.35321340.31842728X-RAY DIFFRACTION89.77
1.79-1.810.34041590.29582919X-RAY DIFFRACTION96.01
1.81-1.840.29111450.27813033X-RAY DIFFRACTION99.66
1.84-1.860.31421590.27432988X-RAY DIFFRACTION99.68
1.86-1.880.2881580.27473097X-RAY DIFFRACTION99.79
1.88-1.910.311640.26353010X-RAY DIFFRACTION99.75
1.91-1.940.29221590.25013024X-RAY DIFFRACTION99.81
1.94-1.970.26311630.24493033X-RAY DIFFRACTION99.81
1.97-20.27031660.24473013X-RAY DIFFRACTION99.47
2-2.040.2611630.23983037X-RAY DIFFRACTION99.01
2.04-2.070.2841710.22752993X-RAY DIFFRACTION99.15
2.07-2.110.28811370.22623017X-RAY DIFFRACTION98.69
2.11-2.160.22331540.23053013X-RAY DIFFRACTION98.11
2.16-2.20.26541740.22792996X-RAY DIFFRACTION97.81
2.2-2.260.2611500.22522886X-RAY DIFFRACTION95.71
2.26-2.310.25341650.22233012X-RAY DIFFRACTION98.51
2.31-2.370.26091510.22453095X-RAY DIFFRACTION99.91
2.37-2.440.26421610.233049X-RAY DIFFRACTION99.88
2.44-2.520.27051610.22463073X-RAY DIFFRACTION99.88
2.52-2.610.25191420.2163072X-RAY DIFFRACTION99.57
2.61-2.720.23121860.21233034X-RAY DIFFRACTION99.44
2.72-2.840.23741770.22343055X-RAY DIFFRACTION99.57
2.84-2.990.28481520.22463046X-RAY DIFFRACTION99.19
2.99-3.180.26381760.22622998X-RAY DIFFRACTION97.24
3.18-3.420.25671620.20873027X-RAY DIFFRACTION97.73
3.42-3.770.22061650.19583115X-RAY DIFFRACTION99.94
3.77-4.310.17681680.16493121X-RAY DIFFRACTION99.31
4.31-5.430.14641770.1363120X-RAY DIFFRACTION98.83
5.43-46.910.2191680.18933259X-RAY DIFFRACTION98.14

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