[English] 日本語
Yorodumi
- PDB-3wov: Crystal structure of the C-terminal globular domain of oligosacch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wov
TitleCrystal structure of the C-terminal globular domain of oligosaccharyltransferase (PaAglB-L, Q9V250_PYRAB, PAB2202) from Pyrococcus abyssi
ComponentsOligosaccharyl transferaseOligosaccharyltransferase
KeywordsTRANSFERASE / oligosaccharide
Function / homology
Function and homology information


dolichyl-phosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / protein glycosylation / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Lipocalin - #390 / Immunoglobulin-like - #3020 / Immunoglobulin-like - #3030 / Oligosaccharyltransferase, peripheral 2 domain / Oligosaccharyltransferase insert domain / Oligosaccharyltransferase Peripheral 2 domain / Oligosaccharyltransferase Insert domain / Rossmann fold - #12610 / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal ...Lipocalin - #390 / Immunoglobulin-like - #3020 / Immunoglobulin-like - #3030 / Oligosaccharyltransferase, peripheral 2 domain / Oligosaccharyltransferase insert domain / Oligosaccharyltransferase Peripheral 2 domain / Oligosaccharyltransferase Insert domain / Rossmann fold - #12610 / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Lipocalin / Immunoglobulin-like / Beta Barrel / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Oligosaccharyl transferase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsMatsuoka, R. / Nyirenda, J. / Maita, N. / Kohda, D.
CitationJournal: To be Published
Title: Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (PaAglB-L, Q9V250_PYRAB, PAB2202) from Pyrococcus abyssi
Authors: Matsuoka, R. / Nyirenda, J. / Maita, N. / Kohda, D.
History
DepositionJan 5, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / software / struct_conn / struct_keywords / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _software.name / _struct_conn.pdbx_dist_value / _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_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oligosaccharyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8482
Polymers57,8081
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.748, 70.748, 204.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Oligosaccharyl transferase / Oligosaccharyltransferase / PaAglB-L / Oligosaccharyl transferase / STT3 subunit


Mass: 57807.734 Da / Num. of mol.: 1 / Fragment: UNP residues 476-976
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Orsay / Gene: PAB2202, PYRAB02240 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V250
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% Jeffamine ED 2001, pH 7.0, 0.1M HEPES, 3% 6-aminohexanoic acid, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.11→204.75 Å / Num. obs: 11310 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 10.3 % / Biso Wilson estimate: 102.75 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.6
Reflection shellRedundancy: 11.2 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
autoPROCdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→23.616 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.81 / SU ML: 0.38 / σ(F): 1.93 / Phase error: 25.47 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 1124 10.02 %RANDOM
Rwork0.2284 10096 --
obs0.2322 11220 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 264.16 Å2 / Biso mean: 116.2318 Å2 / Biso min: 33.35 Å2
Refinement stepCycle: LAST / Resolution: 3.11→23.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3649 0 1 0 3650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033737
X-RAY DIFFRACTIONf_angle_d0.815068
X-RAY DIFFRACTIONf_chiral_restr0.031556
X-RAY DIFFRACTIONf_plane_restr0.003640
X-RAY DIFFRACTIONf_dihedral_angle_d13.7231366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.11-3.25120.34521350.287312241359100
3.2512-3.42220.34141370.286512421379100
3.4222-3.63590.31041410.26312381379100
3.6359-3.91540.25421390.247612611400100
3.9154-4.30730.25171390.211712401379100
4.3073-4.92560.24591410.196212721413100
4.9256-6.18730.24391480.233912901438100
6.1873-23.61680.26831440.21921329147397
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)
15.38492.6258-0.74811.5618-1.04074.52990.1618-1.8439-0.01080.9985-0.43060.21930.0760.13750.0951.4565-0.11160.09511.18180.07850.8105-35.304817.7946-2.4735
28.40163.76670.89631.29680.44253.8666-0.2938-0.6421-0.82410.35160.1494-0.23320.70330.28510.16831.06290.1047-0.01460.63260.1290.747-22.22117.5187-12.7406
38.43213.2302-0.29834.5051.04198.00190.1653-0.54920.06460.3951-0.053-0.572-0.55381.16820.03970.9547-0.0991-0.07970.863-0.0140.9067-9.057430.0185-18.7527
45.0803-1.41841.86491.5846-0.34495.1133-0.09190.29850.17640.0043-0.09550.0388-0.0897-0.76930.17391.0037-0.0453-0.0030.7411-0.02980.7421-42.538828.5176-23.4068
54.1351-0.2202-2.01020.9105-0.77015.5396-0.5064-0.2574-0.73020.22660.0182-0.06680.4929-0.56510.2080.6819-0.1309-0.02010.74740.00640.7492-50.873716.4547-14.7518
64.4477-0.7062-1.62251.51650.65153.9847-0.6438-0.0291-1.6723-0.22530.00910.45520.9794-0.66130.28131.3185-0.29010.29340.6223-0.00661.2002-44.9724.942-15.434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 492:550)A492 - 550
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 551:617)A551 - 617
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 618:690)A618 - 690
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 691:804)A691 - 804
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 805:850)A805 - 850
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 851:970)A851 - 970

+
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