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- PDB-3opu: Crystal structure of the C-terminal domain of Streptococcus mutan... -

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Basic information

Entry
Database: PDB / ID: 3opu
TitleCrystal structure of the C-terminal domain of Streptococcus mutans surface protein SpaP
ComponentsSpaP
KeywordsCELL ADHESION
Function / homology
Function and homology information


endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / ER to Golgi transport vesicle membrane / membrane fusion / 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 / 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
Major cell-surface adhesin PAc
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.181 Å
AuthorsNylander, A. / Persson, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of the C-terminal domain of the surface antigen SpaP from the caries pathogen Streptococcus mutans.
Authors: Nylander, A. / Forsgren, N. / Persson, K.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SpaP
B: SpaP
C: SpaP
D: SpaP
E: SpaP
F: SpaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,43318
Polymers227,9526
Non-polymers48112
Water9,818545
1
A: SpaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0723
Polymers37,9921
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SpaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0723
Polymers37,9921
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SpaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0723
Polymers37,9921
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SpaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0723
Polymers37,9921
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: SpaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0723
Polymers37,9921
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: SpaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0723
Polymers37,9921
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.775, 238.391, 78.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
SpaP


Mass: 37992.066 Da / Num. of mol.: 6 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Details: The strain originates from Dr. Mogens Kilian's culture collection (Aarhus University, Denmark). The strain does not exist in taxonomy database at the time of deposition.
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: Streptococcus mutans SK773 / Gene: SpaP / Plasmid: pET-M11 / Production host: Escherichia coli (E. coli) / Strain (production host): PlysS / References: UniProt: P11657*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate pH 5.0, 15% (w/v) polyethylene glycol 6000., VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.9085 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2010
RadiationMonochromator: Bent silicon crystal, horizontally focusing (R = 12 m).
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9085 Å / Relative weight: 1
ReflectionResolution: 2.18→29.5 Å / Num. all: 132886 / Num. obs: 130690 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 28.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2WZA

2wza


Resolution: 2.181→29.006 Å / SU ML: 0.34 / σ(F): 0.02 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 6626 5.07 %Shells
Rwork0.2104 ---
all0.2124 132886 --
obs0.2124 130690 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.579 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3178 Å2-0 Å20 Å2
2---1.6192 Å2-0 Å2
3---3.9369 Å2
Refinement stepCycle: LAST / Resolution: 2.181→29.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16030 0 12 545 16587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116330
X-RAY DIFFRACTIONf_angle_d1.22822183
X-RAY DIFFRACTIONf_dihedral_angle_d17.7245831
X-RAY DIFFRACTIONf_chiral_restr0.0842519
X-RAY DIFFRACTIONf_plane_restr0.0052884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1813-2.206100.24533834X-RAY DIFFRACTION88
2.2061-2.232100.24384000X-RAY DIFFRACTION91
2.2321-2.259300.23584320X-RAY DIFFRACTION98
2.2593-2.28780.31986830.24253302X-RAY DIFFRACTION92
2.2878-2.317900.24524321X-RAY DIFFRACTION97
2.3179-2.349700.22134255X-RAY DIFFRACTION98
2.3497-2.38320.28877300.22153624X-RAY DIFFRACTION98
2.3832-2.418800.23784291X-RAY DIFFRACTION99
2.4188-2.456600.22594328X-RAY DIFFRACTION98
2.4566-2.49680.29996680.22873639X-RAY DIFFRACTION98
2.4968-2.539800.22254333X-RAY DIFFRACTION98
2.5398-2.58600.22874317X-RAY DIFFRACTION98
2.586-2.63570.28495980.23413753X-RAY DIFFRACTION99
2.6357-2.689500.22834370X-RAY DIFFRACTION99
2.6895-2.74790.26635170.22473843X-RAY DIFFRACTION99
2.7479-2.811800.22614377X-RAY DIFFRACTION99
2.8118-2.8820.28345120.23523884X-RAY DIFFRACTION99
2.882-2.959900.23634378X-RAY DIFFRACTION99
2.9599-3.04690.28164200.24083964X-RAY DIFFRACTION99
3.0469-3.145100.23234449X-RAY DIFFRACTION100
3.1451-3.25740.25293970.21964033X-RAY DIFFRACTION100
3.2574-3.387600.21874424X-RAY DIFFRACTION100
3.3876-3.54150.24193530.20554064X-RAY DIFFRACTION100
3.5415-3.72790.23263120.18934151X-RAY DIFFRACTION100
3.7279-3.96090.19282850.17964163X-RAY DIFFRACTION100
3.9609-4.26590.17812220.15974252X-RAY DIFFRACTION100
4.2659-4.69350.16652040.14524305X-RAY DIFFRACTION100
4.6935-5.3690.15421780.14454327X-RAY DIFFRACTION100
5.369-6.75030.19782600.16464313X-RAY DIFFRACTION100
6.7503-29.00820.19132870.16514450X-RAY DIFFRACTION99

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