[English] 日本語
Yorodumi
- PDB-4tsh: A Novel Protein Fold Forms an Intramolecular Lock to Stabilize th... -

+
Open data


ID or keywords:

Loading...

-
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


protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / extracellular region / metal ion binding / identical protein binding / membrane
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
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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more