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- PDB-4jfx: Structure of phosphotyrosine (pTyr) scaffold bound to pTyr peptide -

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Basic information

Entry
Database: PDB / ID: 4jfx
TitleStructure of phosphotyrosine (pTyr) scaffold bound to pTyr peptide
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Phosphopeptide
KeywordsIMMUNE SYSTEM / immmunoglobulin domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Structure summary
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Mar 26, 2014Group: Source and taxonomy
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,3037
Polymers97,9145
Non-polymers3882
Water17,601977
1
A: Fab light chain
B: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4463
Polymers48,2522
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-21 kcal/mol
Surface area20290 Å2
MethodPISA
2
L: Fab light chain
H: Fab heavy chain
P: Phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8574
Polymers49,6623
Non-polymers1941
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-25 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.854, 152.854, 85.294
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11L-417-

HOH

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Components

#1: Antibody Fab light chain / Fragment antigen-binding


Mass: 23303.885 Da / Num. of mol.: 2
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 / Fragment antigen-binding


Mass: 24947.973 Da / Num. of mol.: 2
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: 1410.465 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 977 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2M KCl, pH 7.5, 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: 1.95→50 Å / Num. all: 83545 / Num. obs: 83545 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.097 / Χ2: 1.063 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.024.10.66882921.0981100
2.02-2.14.10.49682991.0841100
2.1-2.24.10.36982631.0771100
2.2-2.314.10.30683221.0821100
2.31-2.464.10.24483011.0911100
2.46-2.654.20.17683361.071100
2.65-2.914.10.11783401.0511100
2.91-3.334.10.07483571.0011100
3.33-4.240.05184241.016199.9
4.2-5040.03386111.058199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ELVESrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43.156 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 4166 4.99 %RANDOM
Rwork0.1629 ---
obs0.1648 83503 99.91 %-
all-83503 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.23 Å2 / Biso mean: 32.9291 Å2 / Biso min: 6.85 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6666 0 26 977 7669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096972
X-RAY DIFFRACTIONf_angle_d1.1969493
X-RAY DIFFRACTIONf_chiral_restr0.0831085
X-RAY DIFFRACTIONf_plane_restr0.0051217
X-RAY DIFFRACTIONf_dihedral_angle_d12.6432561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9501-1.97220.28411420.23872613275599
1.9722-1.99540.25931160.226626372753100
1.9954-2.01980.28011240.226926462770100
2.0198-2.04530.24141390.21926362775100
2.0453-2.07230.28881390.208926012740100
2.0723-2.10060.26461270.20926512778100
2.1006-2.13070.2361520.195426142766100
2.1307-2.16250.23291520.187526032755100
2.1625-2.19620.24011450.180226052750100
2.1962-2.23220.22231270.187526352762100
2.2322-2.27070.23351350.181226322767100
2.2707-2.3120.23691420.181426462788100
2.312-2.35650.24861520.178426002752100
2.3565-2.40460.24611300.174826512781100
2.4046-2.45690.24331500.170426102760100
2.4569-2.5140.21061440.165326252769100
2.514-2.57690.2491290.168426712800100
2.5769-2.64650.19671240.164726532777100
2.6465-2.72440.20281450.169426222767100
2.7244-2.81230.19761430.175826472790100
2.8123-2.91280.22521320.171626412773100
2.9128-3.02940.19431550.168326282783100
3.0294-3.16730.23351400.170626532793100
3.1673-3.33420.20051240.163526602784100
3.3342-3.5430.1751490.15526562805100
3.543-3.81640.18121540.149426612815100
3.8164-4.20020.17981330.134126712804100
4.2002-4.80720.13451480.110826772825100
4.8072-6.0540.16171200.126327312851100
6.054-43.16680.15911540.15732761291599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9586-0.3070.25332.0512-0.32211.1642-0.01020.0675-0.0403-0.02030.0003-0.1490.1450.1625-00.1859-0.0053-0.02240.1789-0.00470.208166.518-35.3478-15.8243
22.78361.13310.20360.80320.24620.9264-0.07960.09960.0765-0.06860.03630.11820.0232-0.2541-0.00040.2392-0.0536-0.0380.24090.02860.263234.2213-21.4234-20.8516
32.59040.7839-0.5580.7992-0.36841.56990.0116-0.23310.0961-0.0228-0.03740.0319-0.04060.072300.18590.0152-0.00210.19280.00470.20368.1138-30.7292-0.3928
42.2449-0.37430.6031.3076-0.65961.3966-0.0074-0.0681-0.0587-0.0134-0.02910.06150.004-0.092900.1964-0.0799-0.01140.2546-0.00090.217332.3114-33.1371-1.7404
50.5825-0.47790.62931.9355-0.73360.83260.07630.00250.0906-0.2963-0.0355-0.1071-0.0345-0.0166-0.00010.32680.0130.01340.15280.01670.260257.9217-6.358-41.9207
61.10940.01941.43061.8796-0.7262.5894-0.1785-0.2618-0.06590.1960.42320.295-0.2428-0.87840.02930.25910.09010.04230.50280.12340.266743.7625-39.4233-43.774
71.36020.13560.21832.9731-0.21352.34850.02960.06920.0616-0.6688-0.0459-0.4962-0.03680.35190.00690.58390.01790.1340.2160.02110.335166.6392-7.5669-55.715
81.7759-0.02631.25121.4629-0.21232.5468-0.2402-0.23050.0305-0.06550.17550.2159-0.4542-0.4041-0.00080.34450.0323-0.05250.37510.03380.245940.3373-30.3782-64.2895
90.20940.18660.0990.41830.0040.1229-0.0119-0.1241-0.90120.1148-0.02150.31430.434-0.07550.38790.5973-0.2257-0.10940.67930.25790.672537.2289-53.2635-51.8385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 125:219 )B125 - 219
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:124 )B1 - 124
3X-RAY DIFFRACTION3( CHAIN A AND RESID 109:214 )A109 - 214
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1:108 )A1 - 108
5X-RAY DIFFRACTION5( CHAIN H AND RESID 125:215 )H125 - 215
6X-RAY DIFFRACTION6( CHAIN H AND RESID 1:124 )H1 - 124
7X-RAY DIFFRACTION7( CHAIN L AND RESID 109:214 )L109 - 214
8X-RAY DIFFRACTION8( CHAIN L AND RESID 1:108 )L1 - 108
9X-RAY DIFFRACTION9( CHAIN P AND ( RESID 2:7 OR RESID 8:8 ) )P2 - 7
10X-RAY DIFFRACTION9( CHAIN P AND ( RESID 2:7 OR RESID 8:8 ) )P8

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