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- PDB-6e36: The structure of the variable domain of Streptococcus intermedius... -

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Basic information

Entry
Database: PDB / ID: 6.0E+36
TitleThe structure of the variable domain of Streptococcus intermedius antigen I/II (Pas)
ComponentsProbable cell-surface antigen I/II
KeywordsCELL ADHESION / Lectin-like Variable Domain
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. / Antigen I/II, N-terminal / Adhesin P1 N-terminal domain / 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 I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Antigen I/II, N-terminal / Adhesin P1 N-terminal domain / 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 / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Probable cell-surface antigen I/II
Similarity search - Component
Biological speciesStreptococcus intermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
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
B: Probable cell-surface antigen I/II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6334
Polymers92,5852
Non-polymers492
Water7,404411
1
A: Probable cell-surface antigen I/II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3172
Polymers46,2921
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable cell-surface antigen I/II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3172
Polymers46,2921
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.038, 91.308, 71.893
Angle α, β, γ (deg.)90.000, 116.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 46292.328 Da / Num. of mol.: 2 / Fragment: residues 282-682
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 (E. coli) / References: UniProt: Q9KW51
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG3350, 250mM MgCl2, 100mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2017 / Details: Si 111
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→45.65 Å / Num. obs: 88963 / % possible obs: 98.9 % / Redundancy: 3 % / Biso Wilson estimate: 27.1 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.051 / Rrim(I) all: 0.09 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7330.9271.645900.5830.6481.13799.8
9.15-45.652.80.0618.55650.9910.0410.07393.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDS20170923data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WD6

2wd6


Resolution: 1.7→45.65 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 10.076 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.119
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4304 4.8 %RANDOM
Rwork0.2175 ---
obs0.219 84631 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.06 Å2 / Biso mean: 38.895 Å2 / Biso min: 22.02 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å2-0 Å2-1.04 Å2
2---0.93 Å20 Å2
3---2.98 Å2
Refinement stepCycle: final / Resolution: 1.7→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6135 0 2 411 6548
Biso mean--30.95 43.4 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026255
X-RAY DIFFRACTIONr_bond_other_d0.0020.025715
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.968468
X-RAY DIFFRACTIONr_angle_other_deg0.938313400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84926.3273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.784151119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5731512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216945
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021151
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 312 -
Rwork0.364 6317 -
all-6629 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2299-0.62871.21740.3041-0.34080.66830.14760.1237-0.1279-0.0201-0.08360.03130.06250.0622-0.0640.22770.01050.00730.2261-0.01230.025831.2038-10.80194.1204
20.785-0.20990.33540.5417-0.1270.1479-0.0101-0.0324-0.02940.01070.02750.0349-0.0257-0.0136-0.01740.2533-0.00250.03560.24730.01320.007951.8205-10.2519-25.5536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A284 - 357
2X-RAY DIFFRACTION1A358 - 430
3X-RAY DIFFRACTION1A431 - 618
4X-RAY DIFFRACTION1A619 - 678
5X-RAY DIFFRACTION2B285 - 348
6X-RAY DIFFRACTION2B349 - 517
7X-RAY DIFFRACTION2B518 - 618
8X-RAY DIFFRACTION2B619 - 677

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