[English] 日本語
Yorodumi
- PDB-8csc: WbbB D232N-Kdo adduct -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8csc
TitleWbbB D232N-Kdo adduct
ComponentsN-acetyl glucosaminyl transferase
KeywordsTRANSFERASE / Glycsoyltransferase / retaining / donor adduct
Function / homologyCapsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / transferase activity / CYTIDINE-5'-MONOPHOSPHATE / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / Putative N-acetyl glucosaminyl transferase
Function and homology information
Biological speciesRaoultella terrigena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsForrester, T.J.B. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04045-2015 Canada
CitationJournal: Nat Commun / Year: 2022
Title: The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.
Authors: Forrester, T.J.B. / Ovchinnikova, O.G. / Li, Z. / Kitova, E.N. / Nothof, J.T. / Koizumi, A. / Klassen, J.S. / Lowary, T.L. / Whitfield, C. / Kimber, M.S.
History
DepositionMay 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetyl glucosaminyl transferase
B: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,50611
Polymers92,2562
Non-polymers1,2509
Water7,494416
1
A: N-acetyl glucosaminyl transferase
hetero molecules

A: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,47010
Polymers92,2562
Non-polymers1,2158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area6140 Å2
ΔGint-61 kcal/mol
Surface area32470 Å2
MethodPISA
2
B: N-acetyl glucosaminyl transferase
hetero molecules

B: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,54112
Polymers92,2562
Non-polymers1,28610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area6230 Å2
ΔGint-77 kcal/mol
Surface area31990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 158.220, 117.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-808-

HOH

21B-808-

HOH

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein N-acetyl glucosaminyl transferase / retaining Kdo transferase


Mass: 46127.781 Da / Num. of mol.: 2 / Mutation: D232N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella terrigena (bacteria) / Gene: wbbB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q6U8B0
#3: Sugar ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O8 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 423 molecules

#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 % / Description: prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M sodium malonate, 100 mM HEPES, 0.5 % Jeffamine ED-2001

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→39.96 Å / Num. obs: 68061 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 36.96 Å2 / Rsym value: 0.038 / Net I/σ(I): 31.8
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 2.07 / Num. unique obs: 5067 / CC1/2: 0.78 / Rsym value: 0.965 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FA1

5fa1


Resolution: 1.9→39.96 Å / SU ML: 0.2319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.862
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 3405 5 %
Rwork0.1871 64656 -
obs0.1887 68061 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.63 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6242 0 77 416 6735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326571
X-RAY DIFFRACTIONf_angle_d0.53968953
X-RAY DIFFRACTIONf_chiral_restr0.0406992
X-RAY DIFFRACTIONf_plane_restr0.00331159
X-RAY DIFFRACTIONf_dihedral_angle_d13.45182329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.34031420.31152680X-RAY DIFFRACTION99.89
1.93-1.960.32691390.30452657X-RAY DIFFRACTION99.86
1.96-1.990.3181410.28322666X-RAY DIFFRACTION99.79
1.99-2.020.3071400.26172660X-RAY DIFFRACTION99.82
2.02-2.050.2511410.24382672X-RAY DIFFRACTION99.82
2.05-2.090.28681400.23072664X-RAY DIFFRACTION99.96
2.09-2.130.26821420.22872691X-RAY DIFFRACTION99.86
2.13-2.170.2461400.22612651X-RAY DIFFRACTION99.86
2.17-2.220.2471410.22122685X-RAY DIFFRACTION99.79
2.22-2.270.30561400.22982648X-RAY DIFFRACTION99.79
2.27-2.330.27041410.22652673X-RAY DIFFRACTION99.72
2.33-2.390.24861410.21562678X-RAY DIFFRACTION99.86
2.39-2.460.26321410.21612681X-RAY DIFFRACTION99.86
2.46-2.540.24551420.21182693X-RAY DIFFRACTION99.96
2.54-2.630.28911410.21522681X-RAY DIFFRACTION99.96
2.63-2.740.25141410.21092690X-RAY DIFFRACTION100
2.74-2.860.29431430.2242706X-RAY DIFFRACTION99.96
2.86-3.020.28441410.21322684X-RAY DIFFRACTION99.93
3.02-3.20.22991420.20382704X-RAY DIFFRACTION99.93
3.2-3.450.18411430.17592710X-RAY DIFFRACTION100
3.45-3.80.1951430.16122725X-RAY DIFFRACTION99.93
3.8-4.350.16161440.14042734X-RAY DIFFRACTION99.83
4.35-5.480.15541460.14282762X-RAY DIFFRACTION99.97
5.48-39.960.20471500.172861X-RAY DIFFRACTION99.57
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)
11.08583987425-0.339631927127-0.1614468140353.06350579569-1.037323634151.981086646680.03581583428850.314866789194-0.0111564050293-0.8839656466390.07422383855790.2531965886340.498412680958-0.307013579693-0.09079296577750.475316138435-0.0851969014505-0.01807061380950.4049974872670.04091587640920.33676855168921.59760875730.1568947931-34.7606803108
22.179054773461.63044270416-0.2290498555642.1146810797-1.270865664022.42861418609-0.0822776639896-0.193228209786-0.1820741941960.8093597433760.08355727776930.1629723596610.0881129622677-0.230571428977-0.007964262479760.404463341188-0.02282510814710.03559601113310.373703689870.03938327316550.26785220861525.599889368724.1821675431-5.16273066107
32.8334286930.696822471519-1.098428447492.18394616215-0.05087246299782.82655739734-0.0592827271787-0.0757213864032-0.213045629845-0.0584374699585-0.00161500193018-0.4401807752830.2046442429620.3397048173180.04391372194530.28453481977-0.01184125941450.07188814662460.3405091518960.02562781135670.38962507641342.105958450521.3865251272-17.2024375614
42.512883755540.175077896907-0.04785530045463.44647994337-1.601766257853.315786147480.0674550686435-0.1197790178180.1737526064370.3156746181720.3099454861210.650936013969-0.154755463514-0.619173677767-0.3092019670890.248725551881-0.032675177870.09649077242120.3877708407520.07786217934330.39175100617616.233969163327.8976500128-9.78142537033
53.593574059540.46487355394-0.4172466591612.92639901513-0.5932070496241.899687532880.166714239408-0.7079749449340.3942286619171.67192433991-0.002969908452360.139403689008-1.35375079659-0.118681685593-0.2095426574681.155752676890.08307071088240.1734902903650.504703606502-0.001260836102850.41659402740824.117975119967.8232573304-12.8489777861
60.9179086211850.549010772237-0.2835670981574.73811881586-2.160037940222.727588323550.0413044536641-0.105691524373-0.02033818606610.4631499359750.1593547139810.359304964887-0.217518840154-0.217658794831-0.2081904940470.2258217117250.05834140942820.04484904286550.260940519490.01990186451130.26597928849823.009965992956.5641931655-25.5297032943
74.08955455-1.547289034840.9836538035613.75873848909-0.9888666511292.53970043673-0.0006357911014470.2027709450820.2770804308660.0676354421056-0.0458313043406-0.340113044866-0.2282423213360.2122547833690.01990655897770.2399310612540.00843373332857-0.02276850829730.237182398334-0.009158173575870.22187458408136.003842116972.9361687566-40.9204703873
81.65265968452-0.4128778219160.1347751243462.90788791721-0.7217718748162.48827281307-0.05078698249240.0793529435283-0.0627533109198-0.04754092097190.5138355818941.25457677005-0.175359815759-0.854799649268-0.2410366958520.2781283615830.122640093824-0.01530764679520.5309411854650.1997441813870.67684077064712.177067547263.980882634-38.2614676219
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 183 )AA1 - 1831 - 183
22chain 'A' and (resid 184 through 222 )AA184 - 222184 - 220
33chain 'A' and (resid 223 through 321 )AA223 - 321221 - 319
44chain 'A' and (resid 322 through 405 )AA322 - 405320 - 394
55chain 'B' and (resid 1 through 94 )BB1 - 941 - 94
66chain 'B' and (resid 95 through 200 )BB95 - 20095 - 200
77chain 'B' and (resid 201 through 321 )BB201 - 321201 - 321
88chain 'B' and (resid 322 through 403 )BB322 - 403322 - 393

+
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