[English] 日本語
Yorodumi
- PDB-2xwg: Crystal structure of sortase C-1 from Actinomyces oris (formerly ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xwg
TitleCrystal structure of sortase C-1 from Actinomyces oris (formerly Actinomyces naeslundii)
ComponentsSORTASE
KeywordsHYDROLASE / FIMBRIAL ASSEMBLY
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
Sortase C / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesACTINOMYCES ORIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPersson, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of the Sortase Acsrtc-1 from Actinomyces Oris
Authors: Persson, K.
History
DepositionNov 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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 / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -6-STRANDED BARREL THIS IS REPRESENTED BY A -5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SORTASE
B: SORTASE
C: SORTASE
D: SORTASE
E: SORTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8179
Polymers130,6565
Non-polymers1604
Water3,963220
1
A: SORTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2113
Polymers26,1311
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SORTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1712
Polymers26,1311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SORTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1712
Polymers26,1311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SORTASE


Theoretical massNumber of molelcules
Total (without water)26,1311
Polymers26,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: SORTASE


Theoretical massNumber of molelcules
Total (without water)26,1311
Polymers26,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.070, 108.230, 143.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7845, -0.4267, -0.4499), (0.2581, -0.8844, 0.3889), (-0.5639, 0.189, 0.804)21.636, 54.5004, -28.3001
2given(0.4229, -0.2829, -0.8609), (-0.2478, -0.9499, 0.1904), (-0.8716, 0.1328, -0.4718)-13.3522, 15.4772, -24.684
3given(-0.977, -0.1644, 0.136), (-0.1064, -0.1766, -0.9785), (0.1849, -0.9704, 0.1551)-9.3367, 36.0191, 31.8539
4given(-0.507, 0.4225, 0.7513), (0.8504, 0.1032, 0.5159), (0.1405, 0.9005, -0.4116)-2.6579, 59.3118, 9.6005

-
Components

#1: Protein
SORTASE


Mass: 26131.248 Da / Num. of mol.: 5 / Fragment: SORTASE, RESIDUES 78-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACTINOMYCES ORIS (bacteria) / Strain: T14V / Description: ISOLATED FROM ORAL CAVITY, DENTAL PLAQUE / Plasmid: PET-M11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q0Z952
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.5 % / Description: NONE
Crystal growDetails: 1.9 M NAFORMATE, 1.9 M KFORMATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.979
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→45.5 Å / Num. obs: 62240 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 35.03 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 91.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W1J

2w1j


Resolution: 2.4→43.674 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 3201 5.2 %
Rwork0.2053 --
obs0.2074 61074 95.59 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.31 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-11.7478 Å20 Å20 Å2
2---13.6598 Å20 Å2
3---1.912 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6957 0 4 220 7181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117114
X-RAY DIFFRACTIONf_angle_d1.4129719
X-RAY DIFFRACTIONf_dihedral_angle_d16.3882619
X-RAY DIFFRACTIONf_chiral_restr0.0931151
X-RAY DIFFRACTIONf_plane_restr0.0071252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.435800.28892329X-RAY DIFFRACTION85
2.4358-2.473900.28432374X-RAY DIFFRACTION86
2.4739-2.51440.3223210.27642037X-RAY DIFFRACTION87
2.5144-2.557800.2692498X-RAY DIFFRACTION91
2.5578-2.604300.27042489X-RAY DIFFRACTION90
2.6043-2.65440.30853390.27582137X-RAY DIFFRACTION92
2.6544-2.708600.26622577X-RAY DIFFRACTION94
2.7086-2.76740.29843190.25752282X-RAY DIFFRACTION94
2.7674-2.831800.27742622X-RAY DIFFRACTION96
2.8318-2.90260.30173050.26232354X-RAY DIFFRACTION96
2.9026-2.981100.25882679X-RAY DIFFRACTION98
2.9811-3.06880.27662690.24312427X-RAY DIFFRACTION97
3.0688-3.167800.24372717X-RAY DIFFRACTION98
3.1678-3.2810.28852680.23932459X-RAY DIFFRACTION99
3.281-3.412300.22072735X-RAY DIFFRACTION99
3.4123-3.56750.25312170.1912526X-RAY DIFFRACTION99
3.5675-3.75550.23472120.18872558X-RAY DIFFRACTION100
3.7555-3.99070.21341700.16722613X-RAY DIFFRACTION100
3.9907-4.29850.1861520.15142644X-RAY DIFFRACTION100
4.2985-4.73070.15781370.13312672X-RAY DIFFRACTION100
4.7307-5.41410.20461040.15092708X-RAY DIFFRACTION100
5.4141-6.8170.20682390.19592631X-RAY DIFFRACTION100
6.817-43.68160.24621490.19282805X-RAY DIFFRACTION99
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)
11.0703-0.12610.03681.10480.22271.2087-0.01680.01130.1005-0.1099-0.06330.1704-0.1461-0.2017-00.13990.0147-0.04150.2282-0.02520.2443-16.376231.234816.998
20.4621-0.1048-0.30731.44550.10671.0227-0.0422-0.02650.03280.08240.0410.103-0.02970.012200.146-0.02950.04210.1928-0.01430.1921-1.506745.443544.2046
30.56510.3027-0.15941.0808-0.27780.51010.0657-0.08740.01870.1583-0.04680.0103-0.1383-0.020300.3150.0043-0.11150.2016-0.03820.2324-41.4076-8.9745-13.9231
40.7609-0.38970.08990.88030.62491.7795-0.09910.0847-0.052-0.11730.11520.0043-0.05590.152500.1903-0.06780.01840.2479-0.00740.21984.716116.52261.5494
51.47760.21440.28340.61820.21810.60190.03680.2343-0.2156-0.3570.0067-0.0585-0.2490.142600.4847-0.0374-0.08080.3869-0.08670.3034-15.8577-2.3879-27.5408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

+
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