[English] 日本語
Yorodumi
- PDB-8a0m: Capsular polysaccharide synthesis multienzyme in complex with cap... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a0m
TitleCapsular polysaccharide synthesis multienzyme in complex with capsular polymer fragment
ComponentsBcs3
KeywordsBIOSYNTHETIC PROTEIN / Bacterial capsule synthesis
Function / homology
Function and homology information


CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / metal ion binding / plasma membrane
Similarity search - Function
Domain of unknown function DUF5776 / Domain of unknown function (DUF5776) / CDP-glycerol glycerophosphotransferase, N-terminal domain / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / : / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase / HAD superfamily ...Domain of unknown function DUF5776 / Domain of unknown function (DUF5776) / CDP-glycerol glycerophosphotransferase, N-terminal domain / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / : / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate / Bcs3
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsCifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon-Roth, I. / Berger, M. ...Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon-Roth, I. / Berger, M. / Claus, H. / DAngelo, C. / Marina, A. / Gerardy-Schahn, R. / Schubert, M. / Guerin, M.E. / Fiebig, T.
Funding support Germany, Spain, United States, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)412824531 Germany
Ministry of Economy and Competitiveness (MINECO)PID2019-105649RB-I00 Spain
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI149297 United States
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: A multi-enzyme machine polymerizes the Haemophilus influenzae type b capsule.
Authors: Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon Roth, I. / Berger, M. / Claus, H. / D'Angelo, C. / Marina, A. / ...Authors: Cifuente, J.O. / Schulze, J. / Bethe, A. / Di Domenico, V. / Litschko, C. / Budde, I. / Eidenberger, L. / Thiesler, H. / Ramon Roth, I. / Berger, M. / Claus, H. / D'Angelo, C. / Marina, A. / Gerardy-Schahn, R. / Schubert, M. / Guerin, M.E. / Fiebig, T.
History
DepositionMay 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 5, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bcs3
B: Bcs3
C: Bcs3
D: Bcs3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)554,61020
Polymers550,1414
Non-polymers4,46816
Water21612
1
A: Bcs3
B: Bcs3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,30510
Polymers275,0712
Non-polymers2,2348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Bcs3
D: Bcs3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,30510
Polymers275,0712
Non-polymers2,2348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.911, 232.806, 129.177
Angle α, β, γ (deg.)90.000, 118.390, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 through 2 and (name N...
d_2ens_1(chain "B" and ((resid 1 through 2 and (name N...
d_3ens_1(chain "C" and (resid 1 through 11 or (resid 12...
d_4ens_1(chain "D" and ((resid 1 through 2 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPLYSA2 - 186
d_12ens_1ILEASPA265 - 273
d_13ens_1SERVALA281 - 291
d_14ens_1SERLYSA337 - 352
d_15ens_1SERVALA357 - 737
d_16ens_1PROARGA752 - 758
d_17ens_1GLULYSA769 - 957
d_18ens_1LYSSERA967 - 1111
d_19ens_1XXXXXXB
d_21ens_1ASPVALC2 - 206
d_22ens_1SERVALC208 - 604
d_23ens_1PROARGC619 - 625
d_24ens_1GLULYSC629 - 817
d_25ens_1LYSSERC820 - 964
d_26ens_1XXXXXXD
d_31ens_1ASPLYSE1 - 185
d_32ens_1ILEASPE261 - 269
d_33ens_1SERVALE277 - 287
d_34ens_1SERLYSE338 - 353
d_35ens_1SERVALE358 - 738
d_36ens_1PROARGE753 - 759
d_37ens_1GLULYSE770 - 958
d_38ens_1LYSSERE968 - 1112
d_39ens_1XXXXXXF
d_41ens_1ASPLYSG2 - 186
d_42ens_1ILEASPG205 - 213
d_43ens_1SERVALG218 - 228
d_44ens_1SERLYSG233 - 248
d_45ens_1SERARGG253 - 640
d_46ens_1GLUSERG642 - 975
d_47ens_1XXXXXXH

NCS oper:
IDCodeMatrixVector
1given(-0.613422188974, -0.770499578023, 0.173330950327), (-0.771206379811, 0.537122532443, -0.341672511158), (0.170158566679, -0.343263434417, -0.923697069811)15.0609273615, -1.23202338796, -42.3931761162
2given(-0.474487621871, -0.00567630741756, 0.880243873154), (0.00812420804738, -0.999964857513, -0.00206905363111), (0.88022468378, 0.00616954402099, 0.474517062698)35.4927661462, 45.687279396, -22.0053427922
3given(0.449977392843, 0.0678960156482, -0.890455207739), (0.768027448059, -0.538214289897, 0.347072351506), (-0.455690887509, -0.840068752669, -0.29433026659)-9.15206479456, 47.0360451219, -28.8350422788

-
Components

#1: Protein
Bcs3 / Bcs3'


Mass: 137535.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: bcs3', bcs3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2ERG0
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-KOF / beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate / (2R,3S,4S)-5-(((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)oxy)-2,3,4-trihydroxypentyl hydrogen phosphate


Mass: 364.240 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H21O12P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.06M Magnesium chloride hexahydrate, 0.06M Calcium chloride dihydrate, 0.1M Imidazole, 0.1M MES monohydrate (acid) pH 6.5, MPD, PEG 1000, PEG 3350 (37.5%(v/v)) protein (9.5mg/ml) and ...Details: 0.06M Magnesium chloride hexahydrate, 0.06M Calcium chloride dihydrate, 0.1M Imidazole, 0.1M MES monohydrate (acid) pH 6.5, MPD, PEG 1000, PEG 3350 (37.5%(v/v)) protein (9.5mg/ml) and purified polymer (produced by the multienzyme in-vitro)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.6→63.94 Å / Num. obs: 76828 / % possible obs: 99.71 % / Redundancy: 7.1 % / Biso Wilson estimate: 100.15 Å2 / CC1/2: 0.988 / Rrim(I) all: 0.1831 / Net I/σ(I): 8.79
Reflection shellResolution: 3.6→3.729 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 7658 / CC1/2: 0.796 / Rrim(I) all: 0.8839 / % possible all: 99.75

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2dialsdata reduction
xia2dialsdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 3.6→63.94 Å / SU ML: 0.4732 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.6007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 3802 4.96 %
Rwork0.2201 72814 -
obs0.2222 76616 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.26 Å2
Refinement stepCycle: LAST / Resolution: 3.6→63.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31944 0 200 12 32156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002632924
X-RAY DIFFRACTIONf_angle_d0.56744908
X-RAY DIFFRACTIONf_chiral_restr0.04254960
X-RAY DIFFRACTIONf_plane_restr0.0045842
X-RAY DIFFRACTIONf_dihedral_angle_d4.91614678
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.839074679165
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.504124700146
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.899801891907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.650.35381370.28922703X-RAY DIFFRACTION99.82
3.65-3.690.371090.28862727X-RAY DIFFRACTION99.54
3.69-3.740.31791300.27692684X-RAY DIFFRACTION99.93
3.74-3.80.32461250.25062719X-RAY DIFFRACTION99.96
3.8-3.850.27771510.24922663X-RAY DIFFRACTION99.93
3.85-3.910.27961320.2552704X-RAY DIFFRACTION99.47
3.91-3.980.29561340.23192675X-RAY DIFFRACTION99.79
3.98-4.050.28721370.21622702X-RAY DIFFRACTION99.96
4.05-4.120.26371600.21072696X-RAY DIFFRACTION99.93
4.12-4.20.27571750.20842624X-RAY DIFFRACTION99.93
4.2-4.290.28761480.21762719X-RAY DIFFRACTION99.9
4.29-4.380.26231340.20482688X-RAY DIFFRACTION99.89
4.38-4.480.25361170.20192724X-RAY DIFFRACTION99.96
4.48-4.590.23791250.19522725X-RAY DIFFRACTION100
4.59-4.720.2491010.19082728X-RAY DIFFRACTION99.96
4.72-4.860.22741620.19532677X-RAY DIFFRACTION100
4.86-5.010.24451270.18732710X-RAY DIFFRACTION99.93
5.01-5.190.24841370.19142712X-RAY DIFFRACTION99.96
5.19-5.40.2461490.19652702X-RAY DIFFRACTION100
5.4-5.640.25151730.20522668X-RAY DIFFRACTION99.96
5.64-5.940.22331680.22112688X-RAY DIFFRACTION100
5.94-6.310.28021250.23622723X-RAY DIFFRACTION100
6.31-6.80.31141230.22912740X-RAY DIFFRACTION100
6.8-7.480.26421870.22882645X-RAY DIFFRACTION99.96
7.48-8.570.22471590.20042714X-RAY DIFFRACTION100
8.57-10.780.22311230.19742743X-RAY DIFFRACTION99.55
10.78-63.940.25851540.25412611X-RAY DIFFRACTION95.34

+
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