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- PDB-6x1w: Structure of pHis Fab (SC56-2) in complex with pHis mimetic peptide -

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Basic information

Entry
Database: PDB / ID: 6x1w
TitleStructure of pHis Fab (SC56-2) in complex with pHis mimetic peptide
Components
  • ACLYana-3-pTza peptide
  • SC56-2 Heavy chain
  • SC56-2 Light chain
KeywordsIMMUNE SYSTEM / Anti-phosphohistidine antibody / post-translational modification
Biological speciesOryctolagus cuniculus (rabbit)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKalagiri, R. / Stanfield, R. / Wilson, I.A. / Hunter, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies.
Authors: Kalagiri, R. / Stanfield, R.L. / Meisenhelder, J. / La Clair, J.J. / Fuhs, S.R. / Wilson, I.A. / Hunter, T.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: SC56-2 Heavy chain
L: SC56-2 Light chain
A: ACLYana-3-pTza peptide


Theoretical massNumber of molelcules
Total (without water)47,8653
Polymers47,8653
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.060, 121.060, 77.956
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody SC56-2 Heavy chain


Mass: 23539.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody SC56-2 Light chain


Mass: 23576.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Protein/peptide ACLYana-3-pTza peptide


Mass: 748.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Sodium cacodylate pH 6.5, 1 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→47.86 Å / Num. obs: 42281 / % possible obs: 99.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.779 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.063 / Rrim(I) all: 0.165 / Net I/av σ(I): 10.6 / Net I/σ(I): 10.6
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.29 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2083 / CC1/2: 0.306 / Rpim(I) all: 0.538 / Rrim(I) all: 1.41 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dtf

5dtf


Resolution: 1.95→47.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 2104 5 %RANDOM
Rwork0.2003 ---
obs0.2024 40140 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.85 Å2 / Biso mean: 30.809 Å2 / Biso min: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.93 Å20 Å2
3----1.86 Å2
Refinement stepCycle: final / Resolution: 1.95→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 32 345 3632
Biso mean--43.87 40.67 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0133346
X-RAY DIFFRACTIONr_bond_other_d0.0370.0172941
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.6584588
X-RAY DIFFRACTIONr_angle_other_deg2.4471.5686862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6745441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17323.095126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81215484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8021510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023756
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02663
X-RAY DIFFRACTIONr_mcbond_it4.0563.1531764
X-RAY DIFFRACTIONr_mcbond_other4.0293.1481762
X-RAY DIFFRACTIONr_mcangle_it5.2524.6872196
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 151 -
Rwork0.321 2913 -
all-3064 -
obs--98.77 %

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