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- PDB-4mls: Crystal structure of the SpyTag and SpyCatcher-deltaN1 complex -

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Basic information

Entry
Database: PDB / ID: 4mls
TitleCrystal structure of the SpyTag and SpyCatcher-deltaN1 complex
Components
  • Fibronectin binding protein
  • SpyTag
KeywordsPEPTIDE BINDING PROTEIN / Isopeptide bond / SpyCatcher / Protein engineering
Function / homology
Function and homology information


Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold ...Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibronectin binding protein
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.984 Å
AuthorsLi, L. / Fierer, J.O. / Rapoport, T.A. / Howarth, M.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural Analysis and Optimization of the Covalent Association between SpyCatcher and a Peptide Tag.
Authors: Li, L. / Fierer, J.O. / Rapoport, T.A. / Howarth, M.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Sep 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_ref_seq_dif
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_ref_seq_dif.details
Revision 1.3Nov 6, 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
A: Fibronectin binding protein
B: SpyTag


Theoretical massNumber of molelcules
Total (without water)11,6682
Polymers11,6682
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-10 kcal/mol
Surface area5400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.129, 30.474, 39.878
Angle α, β, γ (deg.)90.00, 98.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

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Components

#1: Protein Fibronectin binding protein


Mass: 10192.143 Da / Num. of mol.: 1 / Fragment: UNP residues 461-552 / Mutation: E473I, Y508M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: CnaB2, fba2 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8G9G1
#2: Protein/peptide SpyTag


Mass: 1475.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.83 Å3/Da / Density % sol: 32.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Sodium Acetate 0.1M pH4.5, NaCl 200mM, PEG3350 30%, Glycerol 5%, VAPOR DIFFUSION, HANGING DROP, temperature 295KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.984→50 Å / Num. all: 5858 / Num. obs: 5530 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 5.2 / Num. unique all: 281 / Rsym value: 0.362 / % possible all: 94.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X5P

2x5p


Resolution: 1.984→39.394 Å / SU ML: 0.3 / σ(F): 1.41 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 246 4.47 %Random
Rwork0.2099 ---
all0.2111 6006 --
obs0.2111 5508 91.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.984→39.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms718 0 0 61 779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008745
X-RAY DIFFRACTIONf_angle_d1.1111014
X-RAY DIFFRACTIONf_dihedral_angle_d12.086267
X-RAY DIFFRACTIONf_chiral_restr0.073116
X-RAY DIFFRACTIONf_plane_restr0.005129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.984-2.49930.33881280.26182548X-RAY DIFFRACTION90
2.4993-39.40220.20411180.1942714X-RAY DIFFRACTION93
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)
16.90222.6094-0.87094.53590.00542.457-0.0550.24490.0921-0.31250.06890.23080.11820.0212-0.00730.28660.0148-0.06080.21080.02120.149681.683749.924612.1716
23.18620.13530.81334.82352.00412.79360.15130.2173-0.0174-0.4093-0.0254-0.3179-0.12420.5686-0.07720.3927-0.0044-0.04020.4680.02410.188488.482155.30863.6921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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