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- PDB-6e3f: The structure of the C-terminal domains (C123) of Streptococcus i... -

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Basic information

Entry
Database: PDB / ID: 6e3f
TitleThe structure of the C-terminal domains (C123) of Streptococcus intermedius antigen I/II (Pas)
ComponentsProbable cell-surface antigen I/II
KeywordsCELL ADHESION / DEv IgG fold
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Cross-wall-targeting lipoprotein motif / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal ...Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Cross-wall-targeting lipoprotein motif / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / Adhesin P1 N-terminal domain / Immunoglobulin-like - #740 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Probable cell-surface antigen I/II
Similarity search - Component
Biological speciesStreptococcus intermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchormann, N. / Deivanayagam, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI105038 United States
CitationJournal: J.Bacteriol. / Year: 2021
Title: Structure-Function Characterization of Streptococcus intermedius Surface Antigen Pas.
Authors: Mieher, J.L. / Schormann, N. / Wu, R. / Patel, M. / Purushotham, S. / Wu, H. / Scoffield, J. / Deivanayagam, C.
History
DepositionJul 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Oct 11, 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
A: Probable cell-surface antigen I/II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0493
Polymers56,9691
Non-polymers802
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.589, 99.589, 514.887
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Probable cell-surface antigen I/II


Mass: 56969.156 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues 747-1241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius (bacteria) / Gene: pas / Plasmid: PET23d / Cell line (production host): BL21(DE3)OneShot / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KW51
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 5.6 Å3/Da / Density % sol: 78.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM Citrate, pH 5.8, 200 mM Ammonium sulfate, 900 mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9719 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9719 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 36912 / % possible obs: 100 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.041 / Rrim(I) all: 0.129 / Χ2: 1.542 / Net I/σ(I): 6.3 / Num. measured all: 531423
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1786 / CC1/2: 0.737 / Rpim(I) all: 0.443 / Χ2: 1.086 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-20002.3.7data scaling
PDB_EXTRACT3.24data extraction
HKL-20002.3.7data reduction
MOLREP10.2.36phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QE5

3qe5


Resolution: 2.7→49.61 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 20.003 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.227
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1820 5 %RANDOM
Rwork0.2148 ---
obs0.2163 34620 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 155.94 Å2 / Biso mean: 72.45 Å2 / Biso min: 28.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.7→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 2 73 3957
Biso mean--93.63 47.68 -
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0143978
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173547
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.6645411
X-RAY DIFFRACTIONr_angle_other_deg0.9521.6478316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2065500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29724.925201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52615661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9991512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024504
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02724
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 115 -
Rwork0.333 2527 -
all-2642 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 23.2926 Å / Origin y: 119.5999 Å / Origin z: 536.6131 Å
111213212223313233
T0.6625 Å20.2784 Å2-0.0758 Å2-0.3787 Å2-0.0299 Å2--0.0367 Å2
L0.7533 °2-0.4406 °2-1.2636 °2-0.4555 °20.9093 °2--2.383 °2
S0.0257 Å °0.139 Å °0.0895 Å °0.31 Å °0.141 Å °-0.1095 Å °0.2141 Å °0.06 Å °-0.1667 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A750 - 911
2X-RAY DIFFRACTION1A912 - 1086
3X-RAY DIFFRACTION1A1087 - 1247

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