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- PDB-6x1u: Structure of pHis Fab (SC39-4) in complex with pHis mimetic peptide -

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Basic information

Entry
Database: PDB / ID: 6x1u
TitleStructure of pHis Fab (SC39-4) in complex with pHis mimetic peptide
Components
  • ACLYana-3-pTza peptide
  • SC39-4 Heavy chain
  • SC39-4 Light chain
KeywordsIMMUNE SYSTEM / Anti-phosphohistidine antibody / post-translational modification
Function / homologyACETATE ION
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.641 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: SC39-4 Heavy chain
L: SC39-4 Light chain
A: SC39-4 Heavy chain
B: SC39-4 Light chain
D: ACLYana-3-pTza peptide
C: ACLYana-3-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,35214
Polymers93,8706
Non-polymers4818
Water17,637979
1
H: SC39-4 Heavy chain
L: SC39-4 Light chain
D: ACLYana-3-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1777
Polymers46,9353
Non-polymers2424
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SC39-4 Heavy chain
B: SC39-4 Light chain
C: ACLYana-3-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1747
Polymers46,9353
Non-polymers2394
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.061, 86.111, 167.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Antibody / Protein/peptide , 3 types, 6 molecules HALBDC

#1: Protein SC39-4 Heavy chain


Mass: 23365.238 Da / Num. of mol.: 2
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 SC39-4 Light chain


Mass: 22821.244 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 987 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 979 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M Sodium acetate pH 4.5, 20 % PEG3000

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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: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.64→46.8 Å / Num. obs: 116971 / % possible obs: 99.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 20.1 Å2 / CC1/2: 0.886 / Rmerge(I) obs: 0.88 / Rpim(I) all: 0.46 / Rrim(I) all: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5698 / CC1/2: 0.492 / Rpim(I) all: 0.805 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dtf

5dtf


Resolution: 1.641→46.8 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 5819 4.98 %
Rwork0.1894 --
obs0.1912 116780 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.641→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 32 979 7415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126679
X-RAY DIFFRACTIONf_angle_d1.3319161
X-RAY DIFFRACTIONf_dihedral_angle_d15.6572415
X-RAY DIFFRACTIONf_chiral_restr0.0821077
X-RAY DIFFRACTIONf_plane_restr0.0081170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.641-1.65950.34881510.3292545X-RAY DIFFRACTION69
1.6595-1.6790.35811920.3083704X-RAY DIFFRACTION98
1.679-1.69950.3622190.29333568X-RAY DIFFRACTION98
1.6995-1.7210.29911870.28423710X-RAY DIFFRACTION98
1.721-1.74370.33521960.27673602X-RAY DIFFRACTION98
1.7437-1.76760.32711880.273700X-RAY DIFFRACTION98
1.7676-1.79280.29861720.24923672X-RAY DIFFRACTION98
1.7928-1.81960.28931640.23893685X-RAY DIFFRACTION98
1.8196-1.8480.26961790.23443696X-RAY DIFFRACTION99
1.848-1.87830.29352060.23553662X-RAY DIFFRACTION99
1.8783-1.91070.28082050.23433674X-RAY DIFFRACTION99
1.9107-1.94540.27591900.24933712X-RAY DIFFRACTION99
1.9454-1.98280.26951780.21443746X-RAY DIFFRACTION99
1.9828-2.02330.2422040.18923709X-RAY DIFFRACTION99
2.0233-2.06730.21251870.19393702X-RAY DIFFRACTION99
2.0673-2.11540.23771840.19423744X-RAY DIFFRACTION100
2.1154-2.16830.26061890.18953787X-RAY DIFFRACTION100
2.1683-2.22690.22621860.19813748X-RAY DIFFRACTION100
2.2269-2.29250.25312000.20023717X-RAY DIFFRACTION100
2.2925-2.36650.22881950.19363731X-RAY DIFFRACTION100
2.3665-2.4510.23711980.19313780X-RAY DIFFRACTION100
2.451-2.54920.2582010.19863768X-RAY DIFFRACTION100
2.5492-2.66520.24651910.18533791X-RAY DIFFRACTION100
2.6652-2.80570.19361960.19063792X-RAY DIFFRACTION100
2.8057-2.98140.2362160.19613756X-RAY DIFFRACTION100
2.9814-3.21160.23612070.18223812X-RAY DIFFRACTION100
3.2116-3.53470.20121940.17533813X-RAY DIFFRACTION100
3.5347-4.04590.18712200.16013782X-RAY DIFFRACTION99
4.0459-5.09640.15582130.133874X-RAY DIFFRACTION100
5.0964-46.80.16652110.16283979X-RAY DIFFRACTION98

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