[English] 日本語
Yorodumi
- PDB-4uw0: Low resolution structure of WbdD with C-terminal bundle ordered t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uw0
TitleLow resolution structure of WbdD with C-terminal bundle ordered to residue 505
ComponentsWBDDWorld Blood Donor Day
KeywordsTRANSFERASE / KINASE / METHYLTRANSFERASE
Function / homology
Function and homology information


methyltransferase activity / methylation / protein kinase activity / ATP binding
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / 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
S-ADENOSYLMETHIONINE / Bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase / Uncharacterized protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.87 Å
AuthorsHagelueken, G. / Huang, H. / Naismith, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: A Coiled-Coil Domain Acts as a Molecular Ruler to Regulate O-Antigen Chain Length in Lipopolysaccharide.
Authors: Hagelueken, G. / Clarke, B.R. / Huang, H. / Tuukkanen, A. / Danciu, I. / Svergun, D.I. / Hussain, R. / Liu, H. / Whitfield, C. / Naismith, J.H.
History
DepositionAug 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Jan 21, 2015Group: Database references
Revision 1.4Apr 25, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Sep 18, 2019Group: Data collection / Database references / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list ..._diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_gene_src_variant / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WBDD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1442
Polymers57,7451
Non-polymers3981
Water0
1
A: WBDD
hetero molecules

A: WBDD
hetero molecules

A: WBDD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,4316
Polymers173,2353
Non-polymers1,1953
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area5810 Å2
ΔGint-38.2 kcal/mol
Surface area68050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.290, 181.290, 181.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

-
Components

#1: Protein WBDD / World Blood Donor Day


Mass: 57745.074 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EC3426_03072 / Variant: 09A(H5) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: A0A446F868, UniProt: A0A7I6GZM0*PLUS
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.39 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 3.87→128.2 Å / Num. obs: 9283 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6

-
Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.87→128.19 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.875 / SU B: 141.891 / SU ML: 0.861 / Cross valid method: THROUGHOUT / ESU R Free: 0.916 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.34096 443 4.8 %RANDOM
Rwork0.26783 ---
obs0.27097 8823 98.44 %-
Displacement parametersBiso mean: 171.205 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.87→128.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 27 0 4074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194181
X-RAY DIFFRACTIONr_bond_other_d0.0040.023900
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9465688
X-RAY DIFFRACTIONr_angle_other_deg0.82238937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.415500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70324.182220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00715672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4371529
X-RAY DIFFRACTIONr_chiral_restr0.0670.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
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_it1.42710.1342006
X-RAY DIFFRACTIONr_mcbond_other1.42710.1342006
X-RAY DIFFRACTIONr_mcangle_it2.36815.22504
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32510.3042175
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: 3.87→3.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 34 -
Rwork0.365 638 -
obs--99.56 %
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)
19.2943-0.51972.95665.612-0.89.3881-0.2239-0.6550.13031.12590.1499-0.03160.3502-0.49440.0741.07530.10420.5370.2328-0.07060.4643-54.26516.38731.492
22.2411-1.40591.94095.7828-3.78476.984-0.23460.70120.2054-0.0443-0.0271-0.14620.0560.14250.26160.59870.0270.34840.4655-0.04540.4652-48.37223.6857.785
37.4495-1.8759-3.71691.9108-1.82758.2691-0.38570.1140.05310.10710.12910.14980.4915-1.03820.25660.5817-0.0934-0.0510.9115-0.04220.7232-58.34330.813-22.007
48.01510.471-4.58752.2870.23482.849-0.31410.3581-0.18610.1760.00450.14430.293-0.39060.30960.588-0.0382-0.20010.74520.1940.6735-50.22732.556-35.955
517.6404-11.7781.259711.8446-4.49873.6175-0.7722-0.92381.19540.26140.9772-0.4930.0929-0.9617-0.2051.04650.0899-0.21012.03180.02811.1217-19.25317.957-5.836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 106
2X-RAY DIFFRACTION2A107 - 309
3X-RAY DIFFRACTION3A310 - 397
4X-RAY DIFFRACTION4A398 - 485
5X-RAY DIFFRACTION5A486 - 507

+
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