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- PDB-3pyw: The structure of the SLH domain from B. anthracis surface array p... -

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Basic information

Entry
Database: PDB / ID: 3pyw
TitleThe structure of the SLH domain from B. anthracis surface array protein at 1.8A
ComponentsS-layer protein sap
KeywordsSTRUCTURAL PROTEIN / SLH-domains / polysaccharide binding / GST-SLH / cell wall / Structural Genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / polysaccharide / S-layer
Function / homology
Function and homology information


S-layer / extracellular region
Similarity search - Function
SbsA, Ig-like domain / Bacterial Ig-like domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Wilton, R. / Kern, J. / Joachimiak, A. / Schneewind, O. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of Surface Layer Homology (SLH) Domains from Bacillus anthracis Surface Array Protein.
Authors: Kern, J. / Wilton, R. / Zhang, R. / Binkowski, T.A. / Joachimiak, A. / Schneewind, O.
History
DepositionDec 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Aug 8, 2012Group: Other
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
A: S-layer protein sap
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0132
Polymers21,9171
Non-polymers961
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.767, 77.767, 100.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-269-

HOH

21A-345-

HOH

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Components

#1: Protein S-layer protein sap / / Surface array protein / Surface layer protein


Mass: 21916.781 Da / Num. of mol.: 1 / Fragment: SLH 1, SLH 2, and SLH 3 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: steme 34F2 / Gene: BAS0841, BA_0885, GBAA_0885, GI:49183865, sap / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49051
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M citrate pH5.5, 2.0M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.8→54.96 Å / Num. all: 27789 / Num. obs: 27750 / % possible obs: 99.86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.83
Reflection shellResolution: 1.8→1.846 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 1.61 / Num. unique all: 2133 / % possible all: 98.55

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→54.96 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.211 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.088 / ESU R Free: 0.087
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18913 1486 5.1 %RANDOM
Rwork0.16561 ---
obs0.16677 27750 99.86 %-
all-27789 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.8→54.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 5 241 1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221392
X-RAY DIFFRACTIONr_bond_other_d0.0010.02945
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9641882
X-RAY DIFFRACTIONr_angle_other_deg0.99332334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8425177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55326.42956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63215247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.165152
X-RAY DIFFRACTIONr_chiral_restr0.0920.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined0.2290.2368
X-RAY DIFFRACTIONr_nbd_other0.1790.21013
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2719
X-RAY DIFFRACTIONr_nbtor_other0.0870.2625
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.254
X-RAY DIFFRACTIONr_mcbond_it1.3991.51127
X-RAY DIFFRACTIONr_mcbond_other0.2611.5363
X-RAY DIFFRACTIONr_mcangle_it1.66521413
X-RAY DIFFRACTIONr_scbond_it3.1773612
X-RAY DIFFRACTIONr_scangle_it4.2534.5469
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 99 -
Rwork0.246 2003 -
obs-2102 98.55 %
Refinement TLS params.Method: refined / Origin x: 2.5995 Å / Origin y: 17.1266 Å / Origin z: 33.8102 Å
111213212223313233
T-0.0416 Å20.0122 Å2-0.0187 Å2--0.0136 Å2-0.02 Å2---0.0199 Å2
L0.81 °20.0521 °20.2523 °2-0.4799 °20.0867 °2--0.5297 °2
S-0.0015 Å °-0.0685 Å °0.0107 Å °-0.0206 Å °0.0194 Å °0.0202 Å °-0.0132 Å °0.0328 Å °-0.018 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 180

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