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- PDB-3g69: The crystal structure of Streptococcus pneumoniae Sortase C provi... -

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Basic information

Entry
Database: PDB / ID: 3g69
TitleThe crystal structure of Streptococcus pneumoniae Sortase C provides novel insights into catalysis as well as pilin substrate specificity
ComponentsSortase C
KeywordsTRANSFERASE / Sortase / Pilus / S. pneumoniae
Function / homology
Function and homology information


Sortase C / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNeiers, F. / Madhurantakam, C. / Falker, S. / Manzano, C. / Dessen, A. / Normark, S. / Henriques-Normark, B. / Achour, A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Two crystal structures of pneumococcal pilus sortase C provide novel insights into catalysis and substrate specificity.
Authors: Neiers, F. / Madhurantakam, C. / Falker, S. / Manzano, C. / Dessen, A. / Normark, S. / Henriques-Normark, B. / Achour, A.
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortase C
B: Sortase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6676
Polymers48,0852
Non-polymers5834
Water8,413467
1
A: Sortase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1382
Polymers24,0421
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sortase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5294
Polymers24,0421
Non-polymers4873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.578, 96.554, 98.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sortase C


Mass: 24042.291 Da / Num. of mol.: 2 / Fragment: UNP residues 47-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0467, srtC / Plasmid: pET24c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A7KT63
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MES pH 7.0 and 1.9 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→49.39 Å / Num. obs: 31946 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.011 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 6.3 / Num. unique all: 4490 / % possible all: 97.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G66

3g66


Resolution: 2→43.6 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / SU B: 4.445 / SU ML: 0.126 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25812 1620 5.1 %5%
Rwork0.19228 ---
obs0.19568 30362 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.036 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 34 467 3577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223177
X-RAY DIFFRACTIONr_angle_refined_deg2.1321.9844332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5295399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84124.897145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41115532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4871516
X-RAY DIFFRACTIONr_chiral_restr0.2260.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022396
X-RAY DIFFRACTIONr_nbd_refined0.240.21551
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22147
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2405
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.216
X-RAY DIFFRACTIONr_mcbond_it1.4011.52031
X-RAY DIFFRACTIONr_mcangle_it2.17623179
X-RAY DIFFRACTIONr_scbond_it3.26531306
X-RAY DIFFRACTIONr_scangle_it4.7254.51146
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 123 -
Rwork0.196 2151 -
obs--97.39 %

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