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- PDB-6x1v: Structure of pHis Fab (SC44-8) in complex with pHis mimetic peptide -

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Basic information

Entry
Database: PDB / ID: 6x1v
TitleStructure of pHis Fab (SC44-8) in complex with pHis mimetic peptide
Components
  • ACLYana-3-pTza peptide
  • SC44-8 Heavy chain
  • SC44-8 Light chain
KeywordsIMMUNE SYSTEM / Anti-phosphohistidine antibody / post-translational modification
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Oct 23, 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
L: SC44-8 Light chain
H: SC44-8 Heavy chain
D: ACLYana-3-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2985
Polymers47,1743
Non-polymers1242
Water2,756153
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)50.408, 66.296, 58.578
Angle α, β, γ (deg.)90.000, 94.944, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Antibody SC44-8 Light chain


Mass: 23008.285 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 SC44-8 Heavy chain


Mass: 23417.227 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 / Details: HP3- 3-Phosphotriazolylalanine / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine pH 9.0, 30 % PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.11→43.84 Å / Num. obs: 21391 / % possible obs: 95.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 19.82 Å2 / CC1/2: 0.932 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.121 / Rrim(I) all: 0.222 / Net I/σ(I): 7.6
Reflection shellResolution: 2.11→2.14 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 863 / CC1/2: 0.32 / Rpim(I) all: 0.643 / Rrim(I) all: 1.06 / % possible all: 79.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dtf

5dtf


Resolution: 2.11→39.8 Å / SU ML: 0.2522 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 1079 5.05 %RANDOM
Rwork0.1774 20284 --
obs0.1796 21363 95.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.43 Å2
Refinement stepCycle: LAST / Resolution: 2.11→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 8 153 3389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00463313
X-RAY DIFFRACTIONf_angle_d0.75854533
X-RAY DIFFRACTIONf_chiral_restr0.0484536
X-RAY DIFFRACTIONf_plane_restr0.0047578
X-RAY DIFFRACTIONf_dihedral_angle_d12.32441969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.20.2641940.22922191X-RAY DIFFRACTION82.25
2.2-2.320.28091210.23122627X-RAY DIFFRACTION98.35
2.32-2.460.30631400.2112572X-RAY DIFFRACTION97.59
2.46-2.650.23861400.20162521X-RAY DIFFRACTION95.58
2.65-2.920.24071550.18722578X-RAY DIFFRACTION98.49
2.92-3.340.23211640.17432534X-RAY DIFFRACTION96.01
3.34-4.210.18451390.14782604X-RAY DIFFRACTION97.17
4.21-39.80.16181260.14852657X-RAY DIFFRACTION97.41

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