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- PDB-1ywm: Crystal structure of the N-terminal domain of group B Streptococc... -

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Basic information

Entry
Database: PDB / ID: 1ywm
TitleCrystal structure of the N-terminal domain of group B Streptococcus alpha C protein
ComponentsC protein alpha-antigen
KeywordsSURFACE ACTIVE PROTEIN / BETA SANDWICH / FIBRONECTIN FOLD / ANTIPARALLEL THREE-HELIX BUNDLE
Function / homology
Function and homology information


Surface Active Protein / Surface Active Protein fold / Surface Active Protein domain / Alpha C protein, N-terminal / AlphaC, C-terminal / ACP, C-terminal domain superfamily / ACP, N-terminal domain superfamily / Alpha C protein N terminal / AlphaC N-terminal domain 2 / : ...Surface Active Protein / Surface Active Protein fold / Surface Active Protein domain / Alpha C protein, N-terminal / AlphaC, C-terminal / ACP, C-terminal domain superfamily / ACP, N-terminal domain superfamily / Alpha C protein N terminal / AlphaC N-terminal domain 2 / : / Rib/alpha/Esp surface antigen / Rib domain / M protein-type anchor domain / YSIRK type signal peptide / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / C protein alpha-antigen
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsAuperin, T.C. / Bolduc, G.R. / Baron, M.J. / Heroux, A. / Filman, D.J. / Madoff, L.C. / Hogle, J.M.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of the N-terminal domain of the group B streptococcus alpha C protein.
Authors: Auperin, T.C. / Bolduc, G.R. / Baron, M.J. / Heroux, A. / Filman, D.J. / Madoff, L.C. / Hogle, J.M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Large, Identical, Tandem Repeating Units in the C Protein Alpha Antigen Gene, Bca, of Group B Streptococci
Authors: Michel, J.L. / Madoff, L.C. / Olson, K. / Kling, D.E. / Kasper, D.L. / Ausubel, F.M.
#2: Journal: Cell.Microbiol. / Year: 2002
Title: The Alpha C Protein Mediates Internalization of Group B Streptococcus within Human Cervical Epithelial Cells
Authors: Bolduc, G.R. / Baron, M.J. / Gravekamp, C. / Lachenauer, C.S. / Madoff, L.C.
#3: Journal: J.Biol.Chem. / Year: 2004
Title: Alpha C Protein of Group B Streptococcus Binds Host Cell Surface Glycosaminoglycan and Enters Cells by an Actin-Dependent Mechanism
Authors: Baron, M.J. / Bolduc, G.R. / Goldberg, M.B. / Auperin, T.C. / Madoff, L.C.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: C protein alpha-antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3614
Polymers22,0231
Non-polymers3383
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.464, 56.464, 271.617
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein C protein alpha-antigen


Mass: 22022.682 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: A909 / Gene: bca / Plasmid: PET24A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q02192
#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.88 Å3/Da / Density % sol: 57 %
Description: The statistics for the Mutant SeMet used for experimental phasing are: resolution range 2.6-30, 97.4% completeness, 8581 reflections, 12.8 redundancy, 6.8 Rsym, 30.7 /
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, PEG4000, DTT, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 19-ID11.01
SYNCHROTRONNSLS X26C20.9763
Detector
TypeIDDetectorDate
SBC-21CCDDec 15, 2000
ADSC QUANTUM 42CCDJun 15, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.011
20.97631
ReflectionResolution: 1.86→40 Å / Num. obs: 19465 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rsym value: 0.053 / Net I/σ(I): 29.88
Reflection shellResolution: 1.86→1.93 Å / Mean I/σ(I) obs: 4.69 / Rsym value: 0.339 / % possible all: 71.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: SAD
Starting model: ALPHA C SELENOMETHIONYL MUTANT (2 SELENIUM ATOMS)

Resolution: 1.86→39.53 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.673 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THERE IS NO SINGLE WELL ORDERED CONFORMATION FOR LEU227. THE REFINEMENT STATISTICS FOR THE MUTANT SEMET SET ARE RESOLUTION RANGE 2.6-12, 0.269 RWORK, 0.308 RFREE, 0.010 RMSD BOND LENGTH AND ...Details: THERE IS NO SINGLE WELL ORDERED CONFORMATION FOR LEU227. THE REFINEMENT STATISTICS FOR THE MUTANT SEMET SET ARE RESOLUTION RANGE 2.6-12, 0.269 RWORK, 0.308 RFREE, 0.010 RMSD BOND LENGTH AND 1.552 RMSD BOND ANGLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2193 10.1 %RANDOM
Rwork0.188 ---
all0.193 19465 --
obs0.193 19465 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.04 Å20 Å2
2--0.09 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.86→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 20 222 1651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211448
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9671964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0155179
X-RAY DIFFRACTIONr_chiral_restr0.1080.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021054
X-RAY DIFFRACTIONr_nbd_refined0.1980.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.226
X-RAY DIFFRACTIONr_mcbond_it3.3321894
X-RAY DIFFRACTIONr_mcangle_it5.1631458
X-RAY DIFFRACTIONr_scbond_it7.8143554
X-RAY DIFFRACTIONr_scangle_it9.6874506
LS refinement shellResolution: 1.86→1.96 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.275 237
Rwork0.216 2135

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