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- PDB-3psq: Crystal structure of Spy0129, a Streptococcus pyogenes class B so... -

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Basic information

Entry
Database: PDB / ID: 3psq
TitleCrystal structure of Spy0129, a Streptococcus pyogenes class B sortase involved in pilus biogenesis
ComponentsHypothetical exported protein
KeywordsHYDROLASE / Sortase fold / Sortase / pilus assembly
Function / homology
Function and homology information


membrane => GO:0016020 / hydrolase activity / metal ion binding
Similarity search - Function
Sortase B, Firmicutes / Sortase B family / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsKang, H.J. / Baker, E.N.
CitationJournal: Plos One / Year: 2011
Title: Crystal structure of Spy0129, a Streptococcus pyogenes class B sortase involved in pilus assembly
Authors: Kang, H.J. / Coulibaly, F. / Proft, T. / Baker, E.N.
History
DepositionDec 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Hypothetical exported protein
B: Hypothetical exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,01832
Polymers47,1552
Non-polymers1,86230
Water3,315184
1
A: Hypothetical exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,53817
Polymers23,5781
Non-polymers96116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypothetical exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,47915
Polymers23,5781
Non-polymers90214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.511, 94.511, 253.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hypothetical exported protein / sortase


Mass: 23577.680 Da / Num. of mol.: 2 / Fragment: residues in UNP 36-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: serotype M1, SF370 / Gene: SPy_0129 / Plasmid: pET32-3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9A1S1

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Non-polymers , 5 types, 214 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10% PEG 3350, 0.2M zinc acetate, 0.1M sodium acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2006 / Details: mirrors
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal, asymetric cut 12.2 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97977 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 25405 / Num. obs: 25357 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 4 / Num. unique all: 2472 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.32→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.553 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R Free: 0.232
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26248 1262 5 %RANDOM
Rwork0.20399 ---
all0.238 25357 --
obs0.20683 23960 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.32→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 57 184 3228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223192
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9474311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.975399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68125.663166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22515600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5141510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022424
X-RAY DIFFRACTIONr_mcbond_it0.9141.51900
X-RAY DIFFRACTIONr_mcangle_it1.7123090
X-RAY DIFFRACTIONr_scbond_it2.48931292
X-RAY DIFFRACTIONr_scangle_it4.0294.51205
LS refinement shellResolution: 2.321→2.381 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 88 -
Rwork0.262 1730 -
obs-1730 99.67 %

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