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- PDB-2o0i: crystal structure of the R185A mutant of the N-terminal domain of... -

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Basic information

Entry
Database: PDB / ID: 2o0i
Titlecrystal structure of the R185A mutant of the N-terminal domain of the 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


extracellular region
Similarity search - Function
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 domain ...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 domain / Rib/alpha/Esp surface antigen / 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
C protein alpha-antigen
Similarity search - Component
Biological speciesStreptococcus agalactiae serogroup Ia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHogle, J.M. / Filman, D.J. / Baron, M.J. / Madoff, L.C. / Iglesias, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Identification of a glycosaminoglycan binding region of the alpha C protein that mediates entry of group B streptococci into host cells.
Authors: Baron, M.J. / Filman, D.J. / Prophete, G.A. / Hogle, J.M. / Madoff, L.C.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: C protein alpha-antigen


Theoretical massNumber of molelcules
Total (without water)19,9241
Polymers19,9241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.700, 55.700, 277.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein C protein alpha-antigen


Mass: 19924.242 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, residues 57-227 / Mutation: R185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup Ia (bacteria)
Species: Streptococcus agalactiae / Strain: 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

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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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M sodium acetate, 10% PEG4000, DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 Å
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 5264 / % possible obs: 100 % / Rmerge(I) obs: 0.143 / Χ2: 1.023 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.210.3474880.951100
3.21-3.340.2654960.9571100
3.34-3.490.2355191.0271100
3.49-3.670.1844911.0031100
3.67-3.90.1555101.0731100
3.9-4.20.1215241.0421100
4.2-4.620.1135271.1111100
4.62-5.270.115281.0541100
5.27-6.610.1295500.9621100
6.61-200.0586311.0461100

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Phasing

Phasing MRRfactor: 0.355 / Cor.coef. Fo:Fc: 0.744
Highest resolutionLowest resolution
Rotation4 Å19.81 Å
Translation4 Å19.81 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YWM

1ywm


Resolution: 3.1→19.84 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.849 / SU B: 43.898 / SU ML: 0.325 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 510 9.8 %RANDOM
Rwork0.245 ---
obs0.247 5200 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.299 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 0 0 1403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221425
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9661939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.3055179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.03526.2564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg3.01615253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.058154
X-RAY DIFFRACTIONr_chiral_restr0.0130.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.021053
X-RAY DIFFRACTIONr_nbd_refined0.2330.2598
X-RAY DIFFRACTIONr_nbtor_refined0.310.21014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.23
X-RAY DIFFRACTIONr_mcbond_it1.6032920
X-RAY DIFFRACTIONr_mcangle_it2.7941457
X-RAY DIFFRACTIONr_scbond_it3.9154567
X-RAY DIFFRACTIONr_scangle_it5.8696482
LS refinement shellResolution: 3.1→3.263 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.355 76 -
Rwork0.357 629 -
obs-705 100 %
Refinement TLS params.Method: refined / Origin x: 21.7291 Å / Origin y: 23.0077 Å / Origin z: 145.4155 Å
111213212223313233
T-0.1572 Å2-0.0141 Å20.0394 Å2--0.1645 Å2-0.0525 Å2---0.1497 Å2
L2.1439 °23.1398 °22.3396 °2-7.9838 °25.4427 °2--4.4749 °2
S0.1227 Å °0.0048 Å °0.05 Å °0.2209 Å °0.0875 Å °-0.2039 Å °0.1859 Å °0.2018 Å °-0.2102 Å °

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