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- PDB-4tsh: A Novel Protein Fold Forms an Intramolecular Lock to Stabilize th... -

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Basic information

Entry
Database: PDB / ID: 4tsh
TitleA Novel Protein Fold Forms an Intramolecular Lock to Stabilize the Tertiary Structure of Streptococcus mutans Adhesin P1
Components(Surface protein adhesin) x 2
KeywordsCELL ADHESION / Adhesin / Streptococcus / Intramolecular Lock / Complex
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
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
Surface protein adhesin
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHeim, K.P. / Kailasan, S. / McKenna, R. / Brady, L.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE21789 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE08007 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)T90 DE021990-03 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: An intramolecular lock facilitates folding and stabilizes the tertiary structure of Streptococcus mutans adhesin P1.
Authors: Heim, K.P. / Crowley, P.J. / Long, J.R. / Kailasan, S. / McKenna, R. / Brady, L.J.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface protein adhesin
B: Surface protein adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1306
Polymers69,0012
Non-polymers1294
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-76 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.521, 68.887, 81.278
Angle α, β, γ (deg.)90.000, 96.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1672-

HOH

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Components

#1: Protein Surface protein adhesin


Mass: 12813.826 Da / Num. of mol.: 1 / Fragment: UNP residues 52-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: NG8 / Gene: spaP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9E3B4
#2: Protein Surface protein adhesin


Mass: 56187.180 Da / Num. of mol.: 1 / Fragment: UNP residues 980-1486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: NG8 / Gene: spaP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9E3B4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 537 / 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: 4.07 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were routinely grown at room temperature using the hanging drop vapor diffusion method by mixing 4uL of concentrated NA1/P3C with a mother liquor solution of 24% polyethylene glycol ...Details: Crystals were routinely grown at room temperature using the hanging drop vapor diffusion method by mixing 4uL of concentrated NA1/P3C with a mother liquor solution of 24% polyethylene glycol (PEG) 4000, 150mM ammonium phosphate, at pH 7.5. Crystals formed as large plate clusters within approximately 2 weeks. Following initial crystal growth, 8uL of a solution containing 45% PEG 4000, 100mM ammonium phosphate, at pH 7.5 was added to the crystal drop to facilitate the removal of water from the crystal and improve diffraction quality by producing a more compact and ordered crystal lattice
PH range: 7.5 / Temp details: Room Temp

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→35.85 Å / Num. obs: 73061 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.5
Reflection shellRedundancy: 3.7 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.07 / % possible all: 97

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QE5

3qe5


Resolution: 2→35.847 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1999 2.74 %Random selection
Rwork0.1696 71020 --
obs0.1706 73019 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 280.67 Å2 / Biso mean: 49.0905 Å2 / Biso min: 17.69 Å2
Refinement stepCycle: final / Resolution: 2→35.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 4 545 5241
Biso mean--29.51 49.84 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0224796
X-RAY DIFFRACTIONf_angle_d1.2386494
X-RAY DIFFRACTIONf_chiral_restr0.053744
X-RAY DIFFRACTIONf_plane_restr0.006857
X-RAY DIFFRACTIONf_dihedral_angle_d13.4281757
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0520.29581390.24944932507197
2.052-2.10740.25141410.227450095150100
2.1074-2.16940.2391420.200250495191100
2.1694-2.23940.23081420.19550575199100
2.2394-2.31950.22721430.182850895232100
2.3195-2.41230.2431420.177150435185100
2.4123-2.52210.20871430.175350575200100
2.5221-2.6550.20641420.165850745216100
2.655-2.82130.20981420.166650615203100
2.8213-3.0390.1871450.162151255270100
3.039-3.34470.21741430.156850565199100
3.3447-3.82820.17181440.150751285272100
3.8282-4.82120.16911450.143751325277100
4.8212-35.85230.23421460.185152085354100
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)
14.49243.07331.25425.7293-1.61482.191-0.0935-0.24920.35430.33690.0148-0.32-0.65230.0956-0.20550.28520.0269-0.02210.1999-0.05620.2908-42.374936.23115.5405
24.5624.9555-5.195.7162-5.48756.18540.5283-0.58580.32260.5325-0.31110.2337-0.55710.4729-0.22540.3694-0.02230.00660.4406-0.01560.2489-62.259920.696941.1686
30.03270.06530.36810.22621.14576.6529-0.48750.97490.1187-0.51510.58520.44620.2487-1.4197-0.11730.4251-0.1961-0.10260.66350.10650.3454-90.4647-3.090862.7459
43.44871.4637-4.56171.4717-2.10336.0546-0.04120.0602-0.2748-0.131-0.3431-0.015-0.22390.48770.39080.34190.0321-0.02790.40960.12070.3602-71.95454.851754.3458
56.89714.1013-5.93595.6992-5.94217.0251-0.3863-0.0622-0.6371-0.2328-0.00310.16190.8254-0.23060.44070.5529-0.21610.01220.3479-0.02840.4354-87.7349-11.800563.522
63.69072.5476-5.10771.6608-3.46857.0917-0.1564-0.1585-0.3014-0.0021-0.0902-0.12880.20050.03020.29770.2877-0.01980.00150.260.06770.2573-67.98228.205340.7122
73.69651.4997-2.33870.8447-1.04722.25220.0786-0.11390.09570.0970.0390.0745-0.0161-0.1449-0.12720.26530.0189-0.03080.2341-0.00120.2211-55.042123.863422.4572
81.8380.8806-0.94091.5863-0.96112.117-0.13610.3102-0.0922-0.24310.18820.09770.303-0.1898-0.06420.2545-0.0314-0.03420.1903-0.0560.2443-41.113326.5656-1.0964
96.69164.1365-4.1743.2915-2.54783.983-0.02290.32220.2033-0.08360.20240.11190.0467-0.0397-0.21530.19990.0161-0.06340.1746-0.02690.1964-31.92136.1838-2.8089
102.87090.5515-1.59991.5624-1.50344.18320.14710.81380.3271-0.0687-0.243-0.2405-0.36390.7063-0.12530.2678-0.09950.00780.8030.0710.3224-8.698347.4789-17.9327
110.56380.0838-0.89950.9382-0.37451.95740.13360.73670.01-0.0663-0.2729-0.2158-0.05981.01440.21770.29610.004-0.00250.99010.0120.3988-0.576540.8163-16.0585
122.14250.5424-0.97481.729-0.43381.07680.41931.01430.684-0.2957-0.2579-0.3584-0.33731.08590.43290.3451-0.17140.13731.17210.16250.4495-5.749152.1642-26.045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 66 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 94 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 112 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 124 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 172 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 980 through 1033 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1034 through 1188 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1189 through 1289 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1290 through 1323 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1324 through 1399 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1400 through 1456 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1457 through 1486 )B0

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