[English] 日本語
Yorodumi
- PDB-4azs: High resolution (2.2 A) crystal structure of WbdD. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4azs
TitleHigh resolution (2.2 A) crystal structure of WbdD.
ComponentsMETHYLTRANSFERASE WBDD
KeywordsTRANSFERASE / KINASE
Function / homology
Function and homology information


3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase / polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase / O antigen biosynthetic process / methyltransferase activity / methylation / protein kinase activity / ATP binding / plasma membrane
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / S-ADENOSYLMETHIONINE / O-antigen chain terminator bifunctional methyltransferase/kinase WbdD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.15 Å
AuthorsHagelueken, G. / Huang, H. / Naismith, J.H.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Structure of Wbdd; a Bifunctional Kinase and Methyltransferase that Regulates the Chain Length of the O Antigen in Escherichia Coli O9A.
Authors: Hagelueken, G. / Huang, H. / Clarke, B.R. / Lebl, T. / Whitfield, C. / Naismith, J.H.
History
DepositionJun 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / 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 / _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: METHYLTRANSFERASE WBDD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,93616
Polymers65,0631
Non-polymers1,87315
Water3,405189
1
A: METHYLTRANSFERASE WBDD
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)803,235192
Polymers780,75612
Non-polymers22,479180
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area69650 Å2
ΔGint-2000.5 kcal/mol
Surface area202760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.220, 159.220, 159.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1480-

SO4

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein METHYLTRANSFERASE WBDD


Mass: 65063.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O9A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47592

-
Non-polymers , 5 types, 204 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.8 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.2→65 Å / Num. obs: 36526 / % possible obs: 100 % / Observed criterion σ(I): 3.2 / Redundancy: 11 % / Rmerge(I) obs: 0.09

-
Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.15→65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.056 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22168 1825 5 %RANDOM
Rwork0.17638 ---
obs0.1786 34701 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.632 Å2
Refinement stepCycle: LAST / Resolution: 2.15→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 107 189 3891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023843
X-RAY DIFFRACTIONr_bond_other_d0.0010.023573
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9715247
X-RAY DIFFRACTIONr_angle_other_deg0.7923.0018126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0165452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06124.216204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1315609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2371526
X-RAY DIFFRACTIONr_chiral_restr0.1020.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214333
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02934
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 124 -
Rwork0.212 2405 -
obs--100 %
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)
10.61750.186-0.01670.776-0.35461.0930.0136-0.01650.0109-0.01870.02410.01020.0098-0.0629-0.03770.08240.0058-0.00090.0981-0.01680.08699.41-39.666-16.573
22.88660.16330.62221.0906-1.08442.6767-0.103-0.1935-0.02670.15160.0707-0.1283-0.10350.15930.03230.12860.0217-0.02010.12720.01480.109624.38-51.1855.688
31.0783-0.26641.63461.2929-0.18872.9342-0.0536-0.03110.0309-0.08160.110.059-0.2173-0.3398-0.05640.12760.0723-0.03610.26480.07310.10730.829-56.37630.053
410.05470.130612.816821.250611.52722.441-0.06340.3750.04710.3032-0.50431.06290.12010.21460.56770.08810.0946-0.11310.3424-0.08830.343733.607-42.437.949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 221
2X-RAY DIFFRACTION2A222 - 316
3X-RAY DIFFRACTION3A317 - 464
4X-RAY DIFFRACTION4A465 - 473

+
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