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- PDB-3rbk: The Type II Crystal Structure of Streptococcus agalactiae Sortase C1 -

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Basic information

Entry
Database: PDB / ID: 3rbk
TitleThe Type II Crystal Structure of Streptococcus agalactiae Sortase C1
ComponentsSortase family protein
KeywordsHYDROLASE / Sortase / Beta-barrel / Pilus-specific sortase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKhare, B. / Narayana, S.V.L.
CitationJournal: Plos One / Year: 2011
Title: Structural differences between the Streptococcus agalactiae housekeeping and pilus-specific sortases: SrtA and SrtC1.
Authors: Khare, B. / Krishnan, V. / Rajashankar, K.R. / I-Hsiu, H. / Xin, M. / Ton-That, H. / Narayana, S.V.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 family protein
B: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8395
Polymers51,5502
Non-polymers2883
Water43224
1
A: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8712
Polymers25,7751
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9673
Polymers25,7751
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.09, 73.38, 127.28
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A6 - 47
2113B6 - 47
1213A60 - 207
2213B60 - 207

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Components

#1: Protein Sortase family protein / Sortase C1


Mass: 25775.227 Da / Num. of mol.: 2 / 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, srtC1 (SAG0647) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue / References: UniProt: Q8E0S7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 100 mM calcium chloride, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→63.64 Å / Num. obs: 15115 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 57.5
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 20.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→63.64 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.873 / SU B: 14.288 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.832 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28229 754 5.1 %RANDOM
Rwork0.24783 ---
obs0.24948 14102 99.79 %-
all-15115 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.794 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.9→63.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 15 24 2948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222976
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.9694045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4523.939132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.21915481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8731520
X-RAY DIFFRACTIONr_chiral_restr0.1220.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212235
X-RAY DIFFRACTIONr_mcbond_it0.9081.51879
X-RAY DIFFRACTIONr_mcangle_it1.77423017
X-RAY DIFFRACTIONr_scbond_it2.37431097
X-RAY DIFFRACTIONr_scangle_it4.3544.51028
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
660tight positional0.090.05
621loose positional0.225
660tight thermal0.170.5
621loose thermal0.1810
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 66 -
Rwork0.366 978 -
obs--99.9 %

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