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- PDB-4jg1: Structure of phosphoserine/threonine (pSTAb) scaffold bound to pT... -

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Basic information

Entry
Database: PDB / ID: 4jg1
TitleStructure of phosphoserine/threonine (pSTAb) scaffold bound to pThr peptide
Components
  • Fab heavy chain
  • Fab light chain
  • Phosphopeptide
KeywordsIMMUNE SYSTEM / immmunoglobulin domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PROPANOIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)49,5844
Polymers49,5103
Non-polymers741
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-33 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.807, 95.591, 119.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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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: 24790.717 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: 1415.465 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.: 621 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG1500, 0.1M PCB, pH 6, 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: Sep 5, 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: 1.55→50 Å / Num. all: 72575 / Num. obs: 72575 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.065 / Χ2: 1.075 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.612.90.50864191.063188.1
1.61-1.673.70.40769631.086195.2
1.67-1.755.20.32672081.085198.2
1.75-1.845.90.22272421.087199
1.84-1.9560.14473021.087199.4
1.95-2.160.09673441.057199.6
2.1-2.326.20.07273711.049199.8
2.32-2.656.40.0674121.099199.9
2.65-3.346.60.05875041.0931100
3.34-506.70.03678101.046199.9

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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
Starting model: pdb entries 3N9G, 2GCY

3n9g

2gcy


Resolution: 1.55→41.143 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.9044 / SU ML: 0.11 / σ(F): 1.36 / Phase error: 16.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1738 3659 5.05 %RANDOM
Rwork0.1507 ---
obs0.1518 72503 97.84 %-
all-72503 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.37 Å2 / Biso mean: 21.011 Å2 / Biso min: 8.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→41.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 5 621 4017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013744
X-RAY DIFFRACTIONf_angle_d1.3535162
X-RAY DIFFRACTIONf_chiral_restr0.083601
X-RAY DIFFRACTIONf_plane_restr0.007668
X-RAY DIFFRACTIONf_dihedral_angle_d13.1741430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5486-1.5690.24851240.24022120224480
1.569-1.59040.2561090.2242411252090
1.5904-1.61320.26041260.21262502262893
1.6132-1.63730.22711400.19572473261394
1.6373-1.66280.22291270.19242624275197
1.6628-1.69010.19561280.18622636276498
1.6901-1.71920.20211470.17372588273598
1.7192-1.75050.20431240.17112705282999
1.7505-1.78420.2231260.15742633275999
1.7842-1.82060.1761510.15812656280799
1.8206-1.86020.18171620.1482612277499
1.8602-1.90350.14961420.150127162858100
1.9035-1.95110.16891480.13932626277499
1.9511-2.00380.15921480.13742678282699
2.0038-2.06280.17361320.136626992831100
2.0628-2.12930.15261330.14226982831100
2.1293-2.20540.16431500.135726802830100
2.2054-2.29370.16041830.141326712854100
2.2937-2.39810.16921270.14327242851100
2.3981-2.52450.17581470.143526952842100
2.5245-2.68270.17991460.148127082854100
2.6827-2.88980.17541550.1527432898100
2.8898-3.18050.16781530.155227452898100
3.1805-3.64050.17711390.142827682907100
3.6405-4.58560.15291400.125727952935100
4.5856-41.15780.15521520.159529383090100
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)
10.81510.29-0.46130.9666-0.82441.3679-0.039-0.0576-0.0281-0.0355-0.0087-0.03360.07820.1583-00.1120.00480.00450.135-0.00510.125827.20331.889248.0527
20.33620.15640.6059-0.0250.29611.67490.0111-0.0129-0.00020.03-0.0023-0.03050.00910.089900.1220.00080.00150.108-0.00960.133519.320734.959713.3892
30.67780.59510.01571.6550.61230.9614-0.011-0.0190.0132-0.06390.0517-0.0485-0.06040.00870.00020.12250.0063-0.00950.11830.00460.128714.255140.261151.7879
40.87470.4953-0.42430.9481-0.29922.09540.0278-0.0256-0.0239-0.0089-0.01090.0540.0972-0.1058-00.1062-0.0021-0.00070.1233-0.01080.12340.177726.06822.2984
50.83040.0163-0.39410.53090.05510.19620.11830.76630.0941-0.4398-0.07210.2011-0.1821-0.76170.01910.19610.0144-0.01510.23320.0270.15555.090234.5624-1.4716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resseq 125:238)H125 - 238
2X-RAY DIFFRACTION2(chain H and resseq 1:124)H1 - 124
3X-RAY DIFFRACTION3(chain L and resseq 109:214)L109 - 214
4X-RAY DIFFRACTION4(chain L and resseq 1:108)L1 - 108
5X-RAY DIFFRACTION5(chain P and resseq 1:9)P1 - 9

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