[English] 日本語
Yorodumi
- PDB-5eq2: Crystal Structure of the SrpA Adhesin from Streptococcus sanguinis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eq2
TitleCrystal Structure of the SrpA Adhesin from Streptococcus sanguinis
ComponentsPlatelet-binding glycoprotein
KeywordsSUGAR BINDING PROTEIN / bacterial adhesin / lectin / immunoglobulin fold / serine-rich repeat
Function / homology
Function and homology information


SrpA-like, SigLec-like domain / GspA/SrpA SigLec-like domain / Ubiquitin-like (UB roll) - #890 / Atypical Rib domain / Atypical Rib domain / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...SrpA-like, SigLec-like domain / GspA/SrpA SigLec-like domain / Ubiquitin-like (UB roll) - #890 / Atypical Rib domain / Atypical Rib domain / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Platelet-binding glycoprotein
Similarity search - Component
Biological speciesStreptococcus sanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLoukachevitch, L.V. / McCulloch, K.M. / Vann, K.R. / Wawrzak, Z. / Anderson, S. / Iverson, T.M.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106987 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI41513 United States
American Heart Association14GRNT20390021 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008320 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32 HL007751 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR026915 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Michigan Economic Development Corporation085P1000817 United States
Department of Veteran's Affairs United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Sialoglycan Binding by the Streptococcus sanguinis SrpA Adhesin.
Authors: Bensing, B.A. / Loukachevitch, L.V. / McCulloch, K.M. / Yu, H. / Vann, K.R. / Wawrzak, Z. / Anderson, S. / Chen, X. / Sullam, P.M. / Iverson, T.M.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.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.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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Platelet-binding glycoprotein
B: Platelet-binding glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,84417
Polymers44,0912
Non-polymers75315
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-56 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.522, 46.769, 64.761
Angle α, β, γ (deg.)90.000, 102.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-774-

HOH

-
Components

#1: Protein Platelet-binding glycoprotein


Mass: 22045.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis (strain SK36) (bacteria)
Strain: SK36 / Gene: srpA, SSA_0829 / Plasmid: pGEX3X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: A3CM52
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.9257.93
22.9257.93
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, sitting drop6.5100 mM Na cacodylate, 0.2 M Ca(CH3CO2)2, 18% PEG 8000. Fully formed crystals were soaked in 2 mM K2OsO4, 5% DMSO overnight
2952vapor diffusion, sitting drop6.5100 mM Na cacodylate, 0.2 M Ca(CH3CO2)2, 18% PEG 8000. Fully formed crystals were soaked in 2 mM K2OsO4, 5% DMSO overnight

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.979
SYNCHROTRONAPS 21-ID-D21.14
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDFeb 19, 2015
MARMOSAIC 300 mm CCD2CCDMar 28, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.141
ReflectionRedundancy: 12.5 % / Number: 329804 / Rmerge(I) obs: 0.101 / Χ2: 1.89 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 26384 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.745010.0472.37714.4
3.764.7410.0582.53314.9
3.293.7610.0832.4115
2.993.2910.122.06615
2.772.9910.1811.65115.1
2.612.7710.2531.49515.1
2.482.6110.3361.37813.5
2.372.4810.3361.3867.5
2.282.3710.3881.3117.4
2.22.2810.4671.2737
ReflectionResolution: 1.77→50 Å / Num. obs: 49646 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 22.46 Å2 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.071 / Rrim(I) all: 0.176 / Χ2: 4.17 / Net I/av σ(I): 29.847 / Net I/σ(I): 9.5 / Num. measured all: 362946
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.77-1.85.624550.640.5340.70598
1.8-1.836.224490.7870.4770.69100
1.83-1.876.624280.8370.4130.73998.5
1.87-1.91724700.9060.3510.8061000.8760.945
1.91-1.957.324540.9340.2741.047990.6950.748
1.95-1.997.424720.9450.2310.9741000.5890.633
1.99-2.047.524400.9520.1931.16199.30.4960.533
2.04-2.17.624900.9690.1611.3611000.4160.447
2.1-2.167.624550.9690.131.34799.60.3350.36
2.16-2.237.624790.9760.1121.51799.70.2870.309
2.23-2.317.624770.9810.11.8911000.2570.275
2.31-2.47.624670.9840.0821.98399.90.2110.227
2.4-2.517.624760.9870.0712.1251000.1820.195
2.51-2.647.625190.9890.0622.5491000.1590.17
2.64-2.817.624760.990.0563.7581000.1450.156
2.81-3.037.625020.9880.055.711000.130.14
3.03-3.337.625170.990.0499.791000.1250.134
3.33-3.817.625120.9890.04613.7931000.1160.125
3.81-4.87.625160.9940.03613.42799.90.0910.098
4.8-507.225920.9940.0314.875990.0750.081

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
SOLVEphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→42.56 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 2334 4.96 %
Rwork0.1749 44701 -
obs0.1765 47035 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.6 Å2 / Biso mean: 29.0813 Å2 / Biso min: 9.11 Å2
Refinement stepCycle: final / Resolution: 1.8→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 39 539 3625
Biso mean--31.77 38.99 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083157
X-RAY DIFFRACTIONf_angle_d0.9064321
X-RAY DIFFRACTIONf_chiral_restr0.063502
X-RAY DIFFRACTIONf_plane_restr0.007579
X-RAY DIFFRACTIONf_dihedral_angle_d9.9411917
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.83680.32771380.249526312769100
1.8368-1.87670.28141320.22582598273099
1.8767-1.92040.23751380.200726312769100
1.9204-1.96840.22461380.19152636277499
1.9684-2.02160.22071370.19526272764100
2.0216-2.08110.21591370.18672617275499
2.0811-2.14830.21521380.177826622800100
2.1483-2.22510.21251540.176826262780100
2.2251-2.31410.22851360.178926432779100
2.3141-2.41950.21471540.184926332787100
2.4195-2.5470.23341330.182726352768100
2.547-2.70660.2261430.184926692812100
2.7066-2.91550.23491470.18492657280499
2.9155-3.20880.22561330.18012640277399
3.2088-3.67290.19311170.16732620273798
3.6729-4.62660.15081230.15012620274396
4.6266-42.57160.18111360.15442556269292
Refinement TLS params.Method: refined / Origin x: 48.7759 Å / Origin y: -4.6818 Å / Origin z: 25.93 Å
111213212223313233
T0.1198 Å20.0199 Å20.0084 Å2-0.1893 Å2-0.0057 Å2--0.121 Å2
L0.6905 °2-0.1458 °20.7313 °2-0.0035 °2-0.141 °2--0.4178 °2
S-0.0623 Å °0.0278 Å °-0.0273 Å °-0.0041 Å °0.0154 Å °-0.01 Å °-0.0169 Å °-0.0035 Å °-0.0177 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA249 - 449
2X-RAY DIFFRACTION1allA501 - 851
3X-RAY DIFFRACTION1allB252 - 444
4X-RAY DIFFRACTION1allB501 - 882
5X-RAY DIFFRACTION1allC1 - 5

+
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://pdbjlvh1.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