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- PDB-6x1t: Structure of pHis Fab (SC50-3) in complex with pHis mimetic peptide -

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Basic information

Entry
Database: PDB / ID: 6x1t
TitleStructure of pHis Fab (SC50-3) in complex with pHis mimetic peptide
Components
  • NM23-1-pTza peptide
  • SC50-3 Heavy chain
  • SC50-3 Light chain
KeywordsIMMUNE SYSTEM / Anti-phosphohistidine antibody / post-translational modification
Biological speciesOryctolagus cuniculus (rabbit)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsKalagiri, R. / Stanfield, R.L. / 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 / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: SC50-3 Heavy chain
L: SC50-3 Light chain
A: SC50-3 Heavy chain
B: SC50-3 Light chain
C: SC50-3 Heavy chain
D: SC50-3 Light chain
E: SC50-3 Heavy chain
F: SC50-3 Light chain
G: SC50-3 Heavy chain
I: SC50-3 Light chain
J: SC50-3 Heavy chain
K: SC50-3 Light chain
M: NM23-1-pTza peptide
N: NM23-1-pTza peptide
O: NM23-1-pTza peptide
P: NM23-1-pTza peptide
Q: NM23-1-pTza peptide
R: NM23-1-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,53235
Polymers286,98618
Non-polymers3,54617
Water3,873215
1
H: SC50-3 Heavy chain
L: SC50-3 Light chain
M: NM23-1-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4486
Polymers47,8313
Non-polymers6173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SC50-3 Heavy chain
B: SC50-3 Light chain
N: NM23-1-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4985
Polymers47,8313
Non-polymers6672
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SC50-3 Heavy chain
D: SC50-3 Light chain
O: NM23-1-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4486
Polymers47,8313
Non-polymers6173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: SC50-3 Heavy chain
F: SC50-3 Light chain
Q: NM23-1-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6408
Polymers47,8313
Non-polymers8095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
G: SC50-3 Heavy chain
I: SC50-3 Light chain
R: NM23-1-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4486
Polymers47,8313
Non-polymers6173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
J: SC50-3 Heavy chain
K: SC50-3 Light chain
P: NM23-1-pTza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0524
Polymers47,8313
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.822, 199.666, 204.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein/peptide , 1 types, 6 molecules MNOPQR

#3: Protein/peptide
NM23-1-pTza peptide


Mass: 1080.030 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 2 types, 12 molecules HACEGJLBDFIK

#1: Antibody
SC50-3 Heavy chain


Mass: 24057.916 Da / Num. of mol.: 6
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
SC50-3 Light chain


Mass: 22693.100 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Sugars , 3 types, 6 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 226 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.8 M Ammonium sulfate, 0.1 M Sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.34→49.62 Å / Num. obs: 155051 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 41.69 Å2 / CC1/2: 0.858 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.052 / Rrim(I) all: 0.189 / Net I/σ(I): 15.7
Reflection shellResolution: 2.34→2.39 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.69 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7691 / CC1/2: 0.344 / Rpim(I) all: 0.526 / Rrim(I) all: 1.77 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dtf

5dtf


Resolution: 2.34→49.62 Å / SU ML: 0.3482 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2689 7567 4.89 %
Rwork0.244 147220 -
obs0.2452 154787 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.33 Å2
Refinement stepCycle: LAST / Resolution: 2.34→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19510 0 219 215 19944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003120285
X-RAY DIFFRACTIONf_angle_d0.681427842
X-RAY DIFFRACTIONf_chiral_restr0.04663387
X-RAY DIFFRACTIONf_plane_restr0.00373509
X-RAY DIFFRACTIONf_dihedral_angle_d15.54137110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.370.36611860.35544100X-RAY DIFFRACTION82.61
2.37-2.390.382260.33964867X-RAY DIFFRACTION99.98
2.39-2.420.34122590.32244907X-RAY DIFFRACTION100
2.42-2.450.33942520.31474858X-RAY DIFFRACTION100
2.45-2.490.34592840.31234904X-RAY DIFFRACTION100
2.49-2.520.33712540.30484882X-RAY DIFFRACTION100
2.52-2.560.3232720.30064861X-RAY DIFFRACTION100
2.56-2.590.34312370.29834881X-RAY DIFFRACTION100
2.59-2.630.37222380.29124962X-RAY DIFFRACTION100
2.63-2.680.3392220.28914891X-RAY DIFFRACTION100
2.68-2.720.33542270.28534965X-RAY DIFFRACTION100
2.72-2.770.34332400.28834903X-RAY DIFFRACTION100
2.77-2.830.35332690.2874856X-RAY DIFFRACTION100
2.83-2.880.31492580.29164938X-RAY DIFFRACTION100
2.88-2.950.32522660.28054866X-RAY DIFFRACTION100
2.95-3.020.31452520.28434930X-RAY DIFFRACTION99.98
3.02-3.090.30462740.27684908X-RAY DIFFRACTION100
3.09-3.170.30292330.26894913X-RAY DIFFRACTION100
3.17-3.270.30052430.26994932X-RAY DIFFRACTION100
3.27-3.370.27782580.26844930X-RAY DIFFRACTION100
3.37-3.490.28892410.25884971X-RAY DIFFRACTION100
3.49-3.630.26442570.24784935X-RAY DIFFRACTION100
3.63-3.80.27552740.23814916X-RAY DIFFRACTION100
3.8-40.2612780.23084959X-RAY DIFFRACTION100
4-4.250.23822460.2064962X-RAY DIFFRACTION100
4.25-4.580.19452420.18394998X-RAY DIFFRACTION100
4.58-5.040.20472910.17964989X-RAY DIFFRACTION100
5.04-5.770.20222660.19925012X-RAY DIFFRACTION100
5.77-7.260.23492700.22435070X-RAY DIFFRACTION99.93
7.26-49.620.21072520.20455154X-RAY DIFFRACTION97.18

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