[English] 日本語
Yorodumi
- PDB-8t28: The crystal structure of SrtC2 sortase from Actinomyces oris -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t28
TitleThe crystal structure of SrtC2 sortase from Actinomyces oris
ComponentsClass C sortase
KeywordsHYDROLASE / structural genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologySortase C / Sortase family / Sortase domain superfamily / Sortase domain / hydrolase activity / membrane / PHOSPHATE ION / Class C sortase
Function and homology information
Biological speciesActinomyces oris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOsipiuk, J. / Chang, C. / Ton-That, H.L. / Ton-That, H. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Molecular basis for dual functions in pilus assembly modulated by the lid of a pilus-specific sortase.
Authors: Chang, C. / Ton-That, H. / Osipiuk, J. / Joachimiak, A. / Das, A. / Ton-That, H.
History
DepositionJun 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Class C sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2475
Polymers23,9861
Non-polymers2614
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.390, 90.390, 101.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-501-

PO4

21A-502-

PO4

31A-503-

CL

41A-504-

CL

51A-688-

HOH

61A-706-

HOH

-
Components

#1: Protein Class C sortase


Mass: 23985.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Three N-terminal residues, SNA, are expression tag (cloning artifact)
Source: (gene. exp.) Actinomyces oris (bacteria) / Gene: CYJ23_09785 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I1IT56
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Sodium Chloride, 0.1 M Na2HPO4:Citric Acid, 20% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→45.24 Å / Num. obs: 14868 / % possible obs: 99.7 % / Redundancy: 20.2 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.027 / Rrim(I) all: 0.127 / Χ2: 1.174 / Net I/av σ(I): 25.8 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.71.1561.087020.5040.8190.4611.2570.82196.8
2.14-2.187.91.17140.4620.7950.4061.1820.90199
2.18-2.229.40.9147210.6770.8980.3110.9710.88799.9
2.22-2.2610.90.8297340.7370.9210.2610.8730.999.7
2.26-2.3112.80.8047220.8250.9510.2330.840.901100
2.31-2.3714.90.6887220.8830.9690.1840.7140.98299.9
2.37-2.4217.60.5677300.940.9840.1380.5850.975100
2.42-2.4922.60.5177330.970.9920.110.5290.995100
2.49-2.5626.30.4537300.9780.9950.090.4621.078100
2.56-2.6526.10.3747240.9880.9970.0740.3811.113100
2.65-2.7425.80.3257460.9860.9970.0650.3311.156100
2.74-2.8524.80.2687310.990.9970.0550.2741.232100
2.85-2.9824.40.2187370.9920.9980.0450.2231.245100
2.98-3.1426.10.1787490.9960.9990.0350.1821.35799.9
3.14-3.3325.50.1417480.9970.9990.0280.1431.441100
3.33-3.5923.60.1177490.9970.9990.0240.1191.439100
3.59-3.9525.70.0927590.99810.0180.0941.43100
3.95-4.5224.80.0747700.99910.0150.0761.33699.9
4.52-5.724.10.0617860.99910.0130.0631.13499.9
5.7-45.2421.50.049861110.0110.051.00399.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.269 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20098 764 5.1 %RANDOM
Rwork0.16688 ---
obs0.16861 14075 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.1→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 12 108 1510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161324
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.6431930
X-RAY DIFFRACTIONr_angle_other_deg0.4911.5513089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.036107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28310240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2532.91743
X-RAY DIFFRACTIONr_mcbond_other2.2532.91743
X-RAY DIFFRACTIONr_mcangle_it3.0894.347927
X-RAY DIFFRACTIONr_mcangle_other3.0884.353928
X-RAY DIFFRACTIONr_scbond_it3.8293.309675
X-RAY DIFFRACTIONr_scbond_other3.7923.299668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5324.78992
X-RAY DIFFRACTIONr_long_range_B_refined6.75637.4971472
X-RAY DIFFRACTIONr_long_range_B_other6.71936.8171447
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 65 -
Rwork0.298 985 -
obs--97.49 %
Refinement TLS params.Method: refined / Origin x: -7.0517 Å / Origin y: 37.0297 Å / Origin z: 34.538 Å
111213212223313233
T0.0653 Å2-0.0255 Å20.0304 Å2-0.0147 Å2-0.0144 Å2--0.0231 Å2
L1.7013 °20.2718 °20.381 °2-1.6826 °20.1602 °2--1.8227 °2
S-0.0471 Å °0.0433 Å °-0.123 Å °-0.0294 Å °0.0257 Å °-0.0957 Å °0.1477 Å °0.0263 Å °0.0214 Å °

+
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