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- PDB-3tb7: The type I crystal structure of Streptococcus agalactiae sortase C1 -

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Basic information

Entry
Database: PDB / ID: 3tb7
TitleThe type I crystal structure of Streptococcus agalactiae sortase C1
ComponentsSortase family protein
KeywordsHYDROLASE / Beta-barrel / Pili biogenesis
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
Sortase C / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Sortase family protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsKhare, B.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structure Analysis of Group B Streptococcus Sortase C1: A Model for the "Lid" Movement upon Substrate Binding.
Authors: Khare, B. / Fu, Z.Q. / Huang, I.H. / Ton-That, H. / Narayana, S.V.
History
DepositionAug 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)25,7751
Polymers25,7751
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.590, 46.930, 66.570
Angle α, β, γ (deg.)90.00, 114.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sortase family protein / Sortase C1 / Pilus-specific sortase


Mass: 25775.227 Da / Num. of mol.: 1 / Fragment: UNP residues 43-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Strain: SAG 2603V/R / Gene: SAG0647 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue
References: UniProt: Q8E0S7, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 20% PEG3350, 0.2 M Tris, 0.2 M ammonium acetate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9748 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9748 Å / Relative weight: 1
ReflectionResolution: 2.45→60.34 Å / Num. all: 8228 / Num. obs: 8218 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 33.5
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 7 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 13.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
SGXPROmodel building
SOLVEphasing
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→27.15 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.846 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.807 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30777 381 4.6 %RANDOM
Rwork0.22815 ---
obs0.23173 7834 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.762 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0.3 Å2
2--0.78 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.45→27.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 0 30 1478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221475
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.9562004
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0745186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.98223.63666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.13215241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6511511
X-RAY DIFFRACTIONr_chiral_restr0.10.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211114
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9421.5932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78221499
X-RAY DIFFRACTIONr_scbond_it2.7933543
X-RAY DIFFRACTIONr_scangle_it4.594.5505
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 21 -
Rwork0.253 572 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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