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- PDB-3gle: Crystal Structure of the Major Pilin from Streptococcus pyogenes ... -

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Basic information

Entry
Database: PDB / ID: 3gle
TitleCrystal Structure of the Major Pilin from Streptococcus pyogenes N168A mutant
ComponentsPilin
KeywordsSTRUCTURAL PROTEIN / All-beta / pili / cell adhesion / isopeptide
Function / homology
Function and homology information


pilus / extracellular region
Similarity search - Function
Sortase B signal domain, QVPTGV class / Immunoglobulin-like - #3050 / Streptococcal pilin isopeptide linker / Streptococcal pilin isopeptide linker superfamily / Spy0128-like isopeptide containing domain / Collagen-binding surface protein Cna, B-type domain / Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKang, H.J. / Baker, E.N.
CitationJournal: To be Published
Title: Intramolecular isopeptide bonds give thermodynamic and proteolytic stability to the major pilin protein of Streptococcus pyogenes
Authors: Kang, H.J. / Baker, E.N.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pilin
B: Pilin
C: Pilin


Theoretical massNumber of molelcules
Total (without water)97,3113
Polymers97,3113
Non-polymers00
Water5,837324
1
A: Pilin


Theoretical massNumber of molelcules
Total (without water)32,4371
Polymers32,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pilin


Theoretical massNumber of molelcules
Total (without water)32,4371
Polymers32,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Pilin


Theoretical massNumber of molelcules
Total (without water)32,4371
Polymers32,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.712, 50.869, 123.200
Angle α, β, γ (deg.)90.00, 104.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pilin / / Pilus backbone structural protein / Lancefield T antigen


Mass: 32436.980 Da / Num. of mol.: 3 / Fragment: Residues 18-308 / Mutation: N168A, D306V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Strain: M1, SF370 / Gene: M5005_Spy0109, spy0128, SPy_0128 / Plasmid: pGEX3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9A1S2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MOPS/KOH pH7.5, 21% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 28, 2008 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 40313 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.06 / Net I/σ(I): 38.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 4012 / Rsym value: 0.395 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0078refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B2N

3b2n


Resolution: 2.19→18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.847 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic, tls refinement / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27783 2028 5 %RANDOM
Rwork0.20508 ---
obs0.20879 38231 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.767 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-1.39 Å2
2--0.25 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.19→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6574 0 0 324 6898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226821
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9589276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.875880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15626.91301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.426151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.332153
X-RAY DIFFRACTIONr_chiral_restr0.0920.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215077
X-RAY DIFFRACTIONr_mcbond_it0.7341.54250
X-RAY DIFFRACTIONr_mcangle_it1.39926978
X-RAY DIFFRACTIONr_scbond_it2.27532571
X-RAY DIFFRACTIONr_scangle_it3.8994.52278
LS refinement shellResolution: 2.187→2.243 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 134 -
Rwork0.254 2588 -
obs--91.68 %
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)
11.4610.05142.13560.2528-0.00183.7182-0.0161-0.085-0.01960.0680.0123-0.0035-0.1196-0.04170.00380.04520.01360.03720.0801-0.01760.0434-8.4177.343-58.52
21.5317-0.16992.34390.2608-0.33284.0867-0.008-0.0434-0.03010.01730.03310.0158-0.0523-0.0315-0.02510.02580.01270.01020.0810.00230.0466-16.3647.904-19.559
30.8889-0.25891.33540.2737-0.32033.94230.00390.01260.0128-0.0243-0.02780.00530.0877-0.08840.02390.0218-0.0080.01510.058300.014-37.66832.036-20.247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 307
2X-RAY DIFFRACTION2B27 - 307
3X-RAY DIFFRACTION3C28 - 307

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