[English] 日本語
Yorodumi
- PDB-3rce: Bacterial oligosaccharyltransferase PglB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rce
TitleBacterial oligosaccharyltransferase PglB
Components
  • Oligosaccharide transferase to N-glycosylate proteins
  • Substrate Mimic Peptide
KeywordsTransferase/Peptide / Oligosaccharyltransferase / Membrane protein / helical bundle / glycosylation / acceptor peptide / Plasma membrane / Transferase-Peptide complex
Function / homology
Function and homology information


undecaprenyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / glycosyltransferase activity / post-translational protein modification / magnesium ion binding / plasma membrane
Similarity search - Function
STT3 subunit PglB, C-terminal beta-barrel domain / STT3/PglB C-terminal beta-barrel domain / : / STT3/PglB/AglB core domain / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal
Similarity search - Domain/homology
Undecaprenyl-diphosphooligosaccharide--protein glycotransferase
Similarity search - Component
Biological speciesCampylobacter lari (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.4 Å
AuthorsLizak, C. / Gerber, S. / Numao, S. / Aebi, M. / Locher, K.P.
CitationJournal: Nature / Year: 2011
Title: X-ray structure of a bacterial oligosaccharyltransferase.
Authors: Lizak, C. / Gerber, S. / Numao, S. / Aebi, M. / Locher, K.P.
History
DepositionMar 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3May 22, 2013Group: Refinement description
Revision 1.4Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oligosaccharide transferase to N-glycosylate proteins
B: Substrate Mimic Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3144
Polymers85,2662
Non-polymers492
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-23 kcal/mol
Surface area30350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.060, 116.100, 175.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAS PER THE AUTHORS CHAIN A FUNCTIONS AS A MONOMER IN THE BIOLOGICAL ASSEMBLY

-
Components

#1: Protein Oligosaccharide transferase to N-glycosylate proteins


Mass: 84411.922 Da / Num. of mol.: 1 / Mutation: K2E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter lari (Campylobacter) / Gene: pglB, Cla_1253 / Production host: Escherichia coli (E. coli) / References: UniProt: B9KDD4
#2: Protein/peptide Substrate Mimic Peptide


Mass: 853.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Corresponds to glycosylation sequon
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFROM A DISTINCT STRAIN OF CAMPYLOBACTER LARI

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.07 Å3/Da / Density % sol: 75.73 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 9.4
Details: 0.1M glycine, 50mM magnesium acetate, 6% Dimethyl sulfoxide (DMSO), 23-34% PEG400, pH 9.4, EVAPORATION, temperature 298K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2010
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. all: 24531 / Num. obs: 24350 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.4→3.6 Å / % possible all: 97.6

-
Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.4→29.978 Å / SU ML: 0.58 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2000 8.39 %RANDOM
Rwork0.2379 ---
obs0.2408 23834 --
all-24531 --
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.192 Å2 / ksol: 0.255 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1787 Å20 Å20 Å2
2--0.4177 Å2-0 Å2
3---1.0199 Å2
Refinement stepCycle: LAST / Resolution: 3.4→29.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5665 0 2 1 5668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115811
X-RAY DIFFRACTIONf_angle_d1.4757870
X-RAY DIFFRACTIONf_dihedral_angle_d17.7242076
X-RAY DIFFRACTIONf_chiral_restr0.093877
X-RAY DIFFRACTIONf_plane_restr0.005969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.52170.40231520.34041657X-RAY DIFFRACTION75
3.5217-3.66250.38862000.29182194X-RAY DIFFRACTION100
3.6625-3.82880.35622040.28172213X-RAY DIFFRACTION100
3.8288-4.03020.3192030.26232214X-RAY DIFFRACTION100
4.0302-4.28210.27132020.22842218X-RAY DIFFRACTION100
4.2821-4.61160.2352040.18992226X-RAY DIFFRACTION100
4.6116-5.07370.21892040.17012224X-RAY DIFFRACTION100
5.0737-5.80320.26912070.21812256X-RAY DIFFRACTION100
5.8032-7.2940.27862080.23172283X-RAY DIFFRACTION100
7.294-29.97960.24892160.26092349X-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)
10.2097-1.2328-0.69597.36644.12682.34290.27010.298-0.1383-0.2644-0.8254-0.3471-0.6277-1.87740.48641.34-0.20170.33331.0363-0.03080.93793.9129-28.00113.8436
21.82540.45480.10741.7258-0.19261.7942-0.10130.2601-0.30330.56810.24650.14460.11460.4463-0.09890.5538-0.12180.06640.3983-0.14940.502316.6834-22.741331.4293
31.5991-1.8219-0.27051.40691.35631.02460.48330.06020.6230.4917-0.40490.6383-0.5136-0.0571-0.03851.0457-0.05270.24310.4277-0.11620.84650.6874-3.190443.013
46.4087-4.17491.31966.41211.58551.55750.5651.4954-2.6739-0.6393-0.87691.74480.06390.31220.31330.4591-0.13560.00571.31750.03370.8463-4.8455-23.392811.2756
52.4237-0.7028-0.41322.01910.86120.9227-0.00450.0953-0.32920.9510.19710.21010.575-0.2515-0.01680.8364-0.04710.17160.382-0.10730.56252.8488-34.525739.9059
61.57361.3471.82931.99041.19612.0866-0.43240.5797-0.17920.06930.35370.3635-0.20420.4599-0.00560.39030.00230.01750.4047-0.10690.436712.2707-17.60772.8118
73.12731.15821.45655.67470.40073.11190.18780.8280.4636-0.7464-0.47250.906-0.59571.06240.32980.5137-0.1017-0.15170.68380.16780.51510.9084-8.0315-8.3391
80.9421-0.10870.34760.5058-0.69193.1476-0.57521.6189-0.1909-0.43010.41830.01660.5336-0.87290.15010.603-0.1131-0.09651.1573-0.35710.53870.6964-27.0989-1.1928
91.9572-0.58261.37035.80562.92.95990.73090.6374-0.42210.3329-0.5569-0.15910.51820.08380.03570.5541-0.0003-0.02980.6563-0.06580.8772-0.5683-50.5654-4.7282
103.0010.2462-0.22820.1857-0.75561.94040.62311.4756-0.53160.2916-0.18590.3452-0.21280.3505-0.21990.4405-0.10150.16480.9734-0.50960.61429.9912-33.409-11.0063
110000000000000000.237-0.8109-0.73960.65140.20411.06077.238-20.90220.363
120000000000000000.3749-0.1716-0.08630.53370.0321.104218.551-8.7287.448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resseq 10:17)B - A10 - 17
2X-RAY DIFFRACTION2(chain A and resseq 2:176)A2 - 176
3X-RAY DIFFRACTION3(chain A and resseq 177:282)A177 - 282
4X-RAY DIFFRACTION4(chain A and resseq 307:324)A307 - 324
5X-RAY DIFFRACTION5(chain A and resseq 325:439)A325 - 439
6X-RAY DIFFRACTION6(chain A and resseq 440:500)A440 - 500
7X-RAY DIFFRACTION7(chain A and resseq 501:560)A501 - 560
8X-RAY DIFFRACTION8(chain A and resseq 561:599)A561 - 599
9X-RAY DIFFRACTION9(chain A and resseq 600:634)A600 - 634
10X-RAY DIFFRACTION10(chain A and resseq 635:711)A635 - 711
11X-RAY DIFFRACTION11(chain A and resseq 725)A725
12X-RAY DIFFRACTION12(chain A and resseq 726)A726

+
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