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- PDB-1ng5: 2.0 A crystal structure of Staphylococcus aureus Sortase B -

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Basic information

Entry
Database: PDB / ID: 1ng5
Title2.0 A crystal structure of Staphylococcus aureus Sortase B
Componentssortase B
KeywordsHYDROLASE / TRANSFERASE / structural genomics / a new fold / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


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
NPQTN specific sortase B / NPQTN specific sortase B
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, R. / Joachimiak, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Structure / Year: 2004
Title: Structures of sortase B from Staphylococcus aureus and Bacillus anthracis reveal catalytic amino acid triad in the active site.
Authors: Zhang, R. / Wu, R. / Joachimiak, G. / Mazmanian, S.K. / Missiakas, D.M. / Gornicki, P. / Schneewind, O. / Joachimiak, A.
History
DepositionDec 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sortase B
B: sortase B


Theoretical massNumber of molelcules
Total (without water)51,2822
Polymers51,2822
Non-polymers00
Water5,531307
1
A: sortase B


Theoretical massNumber of molelcules
Total (without water)25,6411
Polymers25,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sortase B


Theoretical massNumber of molelcules
Total (without water)25,6411
Polymers25,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.158, 104.383, 58.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsSortase B existed as monomer, There are two molecules (A,B) in asymmetric unit.

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Components

#1: Protein sortase B


Mass: 25641.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: N315 / Gene: SA0982 / Plasmid: PDM 68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q7A650, UniProt: A0A0H3JPP1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.5M Na2SO4, 0.1M triNa citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.4 Msodium sulfate1reservoir
2100 mMsodium citrate1reservoirpH5.6
32 mMprotein1drop
410 mMTris-HCl1droppH7.5
520 mM1dropNaCl
61 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Nov 19, 2001 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.946561
ReflectionResolution: 1.97→50 Å / Num. all: 31422 / Num. obs: 29674 / % possible obs: 94.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 6 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13
Reflection shellResolution: 1.97→2.05 Å / Redundancy: 4.81 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.63 / Num. unique all: 2739 / % possible all: 79.5
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.11

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Processing

Software
NameVersionClassification
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→42.09 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The number of reflections for refinement is greater than the number of reflections for data collection, because in CNS (hlml taget) refinement, the Friedel's pair was treated as two seperated reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2466 4.9 %RANDOM
Rwork0.237 ---
obs0.237 50697 89.6 %-
all-56561 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.368 Å2 / ksol: 0.431764 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1-11.56 Å20 Å20 Å2
2---8.3 Å20 Å2
3----3.26 Å2
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 0 307 3799
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 348 5 %
Rwork0.352 6563 -
obs--73.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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