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- PDB-8uhs: anti-Phosphohistidine Fab hSC44.ck.20.elbow bound to phosphate -

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Basic information

Entry
Database: PDB / ID: 8uhs
Titleanti-Phosphohistidine Fab hSC44.ck.20.elbow bound to phosphate
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
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7034
Polymers47,5462
Non-polymers1572
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-26 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.326, 72.326, 205.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-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
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
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: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.4→49.79 Å / Num. obs: 22383 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 51.14 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.023 / Rrim(I) all: 0.075 / Rsym value: 0.071 / Χ2: 1.64 / Net I/σ(I): 42
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 1088 / CC1/2: 0.805 / CC star: 0.944 / Rpim(I) all: 0.322 / Rrim(I) all: 0.83 / Rsym value: 0.761 / Χ2: 1.175 / % possible all: 99.7

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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: 2.4→49.79 Å / SU ML: 0.4391 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.9277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2863 1079 4.84 %
Rwork0.2517 21221 -
obs0.2534 22300 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.75 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 9 24 3317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213368
X-RAY DIFFRACTIONf_angle_d0.5354576
X-RAY DIFFRACTIONf_chiral_restr0.0422515
X-RAY DIFFRACTIONf_plane_restr0.0045583
X-RAY DIFFRACTIONf_dihedral_angle_d12.81291195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.4371340.36142549X-RAY DIFFRACTION98.71
2.51-2.640.37041490.32792573X-RAY DIFFRACTION99.96
2.64-2.80.37811190.34592617X-RAY DIFFRACTION100
2.8-3.020.36451220.30852649X-RAY DIFFRACTION100
3.02-3.320.33081370.29342613X-RAY DIFFRACTION100
3.32-3.80.32461380.28052654X-RAY DIFFRACTION100
3.81-4.790.21891380.20732691X-RAY DIFFRACTION99.86
4.79-49.790.23781420.19762875X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.758362556720.904667141693-0.4236149582812.72321365279-0.4111764025480.420622928350.02252509543770.126953302682-0.4092392432130.368624250561.160839298190.405511277782-0.197867533914-1.39139942182-0.3660226617580.5203336164290.1239426248580.07281155033131.005538348870.4229404844170.671487117452-3.32595210536-35.31706537034.42145732941
21.50607606778-0.6622744018320.535345032140.7034711957840.7879918455482.70792492355-0.1959909590020.04161283315440.0914233393221-0.3138221883060.1980579621460.06030581203740.000862244811093-0.162051392563-0.02155418659730.437258447102-0.0172976658824-0.01139317376320.3457621280140.07191983425220.37126695544614.2483656764-27.3299034939-22.2333496639
31.65319592289-0.154117957369-0.1033276346712.35180963158-0.2618905187191.38095771872-0.302870604929-0.093721641228-0.04168981032840.358150616060.205596197361-0.3054748331450.2014647001970.1042241488960.06470146120990.51120834761-0.021234476684-0.02217176644190.262800311681-0.05034818392490.36883443434819.9406906225-25.3141299259-20.4368528993
40.07960050166160.0228565098644-0.04890558096870.802478621899-0.5284034150331.900057237610.435656644013-0.2499605881920.8181191650361.492627835550.7867109869341.51488332634-1.77098124247-0.940724896340.1773665355921.608149866280.7579049732120.8235583403450.7016733895620.069803559620.822846852332-0.437541332985-13.80679518667.00254899725
51.783686692240.4470265911560.2419723279623.19926677498-0.382797808212.176351572140.001180296251970.03097000844320.07464313616480.04117685897110.3018363099460.280883894754-0.199398409229-0.112528911994-0.2791557396170.499949037429-0.0124613369210.003307944486320.271882249040.03899009508280.39286195675711.2663924491-13.1217779872-27.7979446703
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 106 )HA1 - 1061 - 110
22chain 'H' and (resid 107 through 133 )HA107 - 133111 - 136
33chain 'H' and (resid 134 through 213 )HA134 - 213137 - 216
44chain 'L' and (resid 1 through 113 )LC1 - 1131 - 119
55chain 'L' and (resid 114 through 212 )LC114 - 212120 - 218

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