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- PDB-4jfz: Structure of phosphoserine (pSAb) scaffold bound to pSer peptide -

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Basic information

Entry
Database: PDB / ID: 4jfz
TitleStructure of phosphoserine (pSAb) scaffold bound to pSer peptide
Components
  • Fab heavy chain
  • Fab light chain
  • Phosphopeptide
KeywordsIMMUNE SYSTEM / Immunoglobulin domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PROPANOIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKoerber, J.T. / Thomsen, N.D. / Hannigan, B.T. / Degrado, W.F. / Wells, J.A.
CitationJournal: Nat.Biotechnol. / Year: 2013
Title: Nature-inspired design of motif-specific antibody scaffolds.
Authors: Koerber, J.T. / Thomsen, N.D. / Hannigan, B.T. / Degrado, W.F. / Wells, J.A.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Mar 26, 2014Group: Source and taxonomy
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
P: Phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6524
Polymers49,5783
Non-polymers741
Water12,160675
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-31 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.504, 94.870, 120.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab light chain


Mass: 23303.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): C43 PRO+
#2: Antibody Fab heavy chain


Mass: 24872.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): C43 PRO+
#3: Protein/peptide Phosphopeptide


Mass: 1401.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 23% PEG1500, 0.1M PCB, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2012
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.75→120.583 Å / Num. all: 51060 / Num. obs: 51060 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.113 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.843.90.71312842872930.71399.5
1.84-1.963.90.4661.52707669670.46699.3
1.96-2.093.90.32.42532265410.399.5
2.09-2.263.90.2153.32361561280.21599.7
2.26-2.473.90.1634.62179056260.16399.6
2.47-2.773.90.1116.72007551490.11199.9
2.77-3.23.90.0788.71766345780.07899.9
3.2-3.913.70.05811.31465039070.05899.8
3.91-5.533.70.0321.51135230780.0399.8
5.53-74.563.70.02623.9670217930.02699.7

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ELVESrefinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→74.56 Å / Occupancy max: 1 / Occupancy min: 0.11 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 17.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 2622 5.14 %RANDOM
Rwork0.1538 ---
obs0.156 50977 99.48 %-
all-50977 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.83 Å2 / Biso mean: 22.1458 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: LAST / Resolution: 1.75→74.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 5 675 4053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013581
X-RAY DIFFRACTIONf_angle_d1.3154901
X-RAY DIFFRACTIONf_chiral_restr0.084567
X-RAY DIFFRACTIONf_plane_restr0.006629
X-RAY DIFFRACTIONf_dihedral_angle_d13.1281325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.78180.35131310.26422474260599
1.7818-1.81610.28921390.23732532267199
1.8161-1.85320.23911470.21192475262299
1.8532-1.89350.21421270.19812539266699
1.8935-1.93750.26821470.1922465261299
1.9375-1.9860.20691430.17452494263799
1.986-2.03970.22381300.16472503263399
2.0397-2.09970.22011240.15692552267699
2.0997-2.16750.20051250.150325292654100
2.1675-2.2450.19421570.144224922649100
2.245-2.33480.16841520.14472504265699
2.3348-2.44110.22981270.14932571269899
2.4411-2.56980.2161390.150325432682100
2.5698-2.73080.19771450.145925492694100
2.7308-2.94170.18741410.148625522693100
2.9417-3.23770.19451400.147225722712100
3.2377-3.70620.1891400.137326042744100
3.7062-4.66940.14391220.121726362758100
4.6694-74.62770.17591460.147427692915100

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