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- PDB-4mli: Crystal structure of the SpyTag/SpyCatcher complex -

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Basic information

Entry
Database: PDB / ID: 4mli
TitleCrystal structure of the SpyTag/SpyCatcher 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: 2.1 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 1.3Oct 16, 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
C: Fibronectin binding protein
B: SpyTag
D: SpyTag


Theoretical massNumber of molelcules
Total (without water)27,7834
Polymers27,7834
Non-polymers00
Water2,864159
1
A: Fibronectin binding protein
B: SpyTag


Theoretical massNumber of molelcules
Total (without water)13,8912
Polymers13,8912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-10 kcal/mol
Surface area5560 Å2
MethodPISA
2
C: Fibronectin binding protein
D: SpyTag


Theoretical massNumber of molelcules
Total (without water)13,8912
Polymers13,8912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-10 kcal/mol
Surface area5620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.621, 38.527, 44.491
Angle α, β, γ (deg.)83.70, 78.25, 89.72
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Fibronectin binding protein


Mass: 12415.537 Da / Num. of mol.: 2 / Fragment: UNP residues 440-552 / 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.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.9 Å3/Da / Density % sol: 35.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Sodium Acetate 0.1M pH4.5, PEG3350 30%, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: 2.1→50 Å / Num. all: 11842 / Num. obs: 9604 / % possible obs: 81.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 23.84 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 9.18
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.4 / Num. unique all: 510 / Rsym value: 0.208 / % possible all: 86.7

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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: 2.1→38.288 Å / SU ML: 0.23 / σ(F): 1.97 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 450 4.94 %random
Rwork0.1983 ---
all0.1996 11935 --
obs0.1996 9109 76.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→38.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 0 159 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041590
X-RAY DIFFRACTIONf_angle_d0.6922183
X-RAY DIFFRACTIONf_dihedral_angle_d12.351598
X-RAY DIFFRACTIONf_chiral_restr0.028254
X-RAY DIFFRACTIONf_plane_restr0.003278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.40320.24951470.19952805X-RAY DIFFRACTION74
2.4032-3.02750.26531540.22553017X-RAY DIFFRACTION80
3.0275-38.29470.20241490.18612837X-RAY DIFFRACTION75
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)
12.00963.2462-8.50782.0034-4.5992.00170.12150.89810.0676-1.40450.09980.82120.1907-0.9603-0.17610.46610.0268-0.00910.5576-0.12830.342144.68458.804868.1701
23.6706-0.35980.64053.56680.11233.267-0.26890.1666-0.6777-0.00240.0273-0.13450.10510.09010.22750.1548-0.0070.0730.1536-0.01060.300358.78535.274678.0098
36.585-4.56133.40412.003-3.23038.1984-0.07870.52480.0244-0.3218-0.36080.20750.0328-0.28980.46250.4766-0.1303-0.0970.4663-0.14150.32450.74613.010362.4459
43.4046-0.8283-0.29183.5918-0.33261.887-0.0586-0.2218-0.41830.4255-0.1722-0.01510.43040.09060.1770.3470.04630.09020.19150.04190.74562.7107-4.370181.5866
54.9348-0.0501-1.24253.16270.08884.0755-0.0492-0.40220.35520.1365-0.0197-0.0217-0.24130.13620.04270.14570.0183-0.01330.15-0.02710.21572.889517.387686.4458
64.98581.0079-1.36843.7568-1.37513.60170.1528-0.16030.6077-0.0784-0.2307-0.2614-0.33390.3706-0.13130.3386-0.0407-0.04340.1908-0.00730.463878.820627.025980.7667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 22:26 )A22 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:94 )A27 - 94
3X-RAY DIFFRACTION3( CHAIN A AND RESID 95:103 )A95 - 103
4X-RAY DIFFRACTION4( CHAIN B AND RESID 111:122 )B111 - 122
5X-RAY DIFFRACTION5( CHAIN C AND RESID 22:104 )C22 - 104
6X-RAY DIFFRACTION6( CHAIN D AND RESID 111:122 )D111 - 122

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