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- PDB-3ipk: Crystal Structure of A3VP1 of AgI/II of Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 3ipk
TitleCrystal Structure of A3VP1 of AgI/II of Streptococcus mutans
ComponentsAgI/II
KeywordsCELL ADHESION / alpha helix / PPII helix / supersandwich fold / surface adhesin / Cell wall / Peptidoglycan-anchor
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 / identical protein binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2200 / Major cell-surface adhesin PAc / Major cell-surface adhesin PAc / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2200 / Major cell-surface adhesin PAc / Major cell-surface adhesin PAc / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Sandwich / Mainly Beta
Similarity search - Domain/homology
phenylmethanesulfonic acid / PA / Surface protein adhesin
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.04 Å
AuthorsLarson, M.R. / Rajashankar, K.R. / Patel, M. / Robinette, R. / Crowley, P. / Michalek, S.M. / Brady, L.J. / Deivanayagam, C.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of alpha- and PPII-helices.
Authors: Larson, M.R. / Rajashankar, K.R. / Patel, M.H. / Robinette, R.A. / Crowley, P.J. / Michalek, S. / Brady, L.J. / Deivanayagam, C.
History
DepositionAug 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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_ref_seq_dif / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AgI/II
B: AgI/II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5218
Polymers108,9052
Non-polymers6176
Water18,1951010
1
A: AgI/II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7614
Polymers54,4521
Non-polymers3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AgI/II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7614
Polymers54,4521
Non-polymers3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.031, 164.146, 67.733
Angle α, β, γ (deg.)90.00, 91.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AgI/II / PA


Mass: 54452.324 Da / Num. of mol.: 2 / Fragment: UNP residues 386-874
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: pa / Plasmid: pMBP-A1VP1-his / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8R5D9, UniProt: C9E3B4*PLUS
#2: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1010 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS THE CONFLICTS AT RESIDUES 398 AND 782 ARE DUE TO STRAIN VARIATION. THE ...ACCORDING TO THE AUTHORS THE CONFLICTS AT RESIDUES 398 AND 782 ARE DUE TO STRAIN VARIATION. THE DEPOSITED SEQUENCE IS FROM THE NG8 STRAIN

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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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% MME PEG 2000, 0.2M Ammonium sulfate, 0.05M Sodium cacodylate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 66337 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 29.3
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 8.88 / Num. unique all: 6271 / Rsym value: 0.182 / % possible all: 91

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementStarting model: PDB entry 1JMM

1jmm


Resolution: 2.04→42.72 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 62608.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 6637 10.1 %RANDOM
Rwork0.181 ---
obs0.181 65452 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4909 Å2 / ksol: 0.328094 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.88 Å20 Å20.03 Å2
2--4.55 Å20 Å2
3----0.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 2.04→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7520 0 34 1010 8564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.04→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 722 10.4 %
Rwork0.182 6212 -
obs--56.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4PMS_par.txtPMS_top.txt

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