[English] 日本語
Yorodumi
- PDB-8hhd: Crystal structure of PaMurU -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hhd
TitleCrystal structure of PaMurU
ComponentsNucleotidyl transferase
KeywordsTRANSFERASE / MurU / N-acetylmuramate alpha-1-phosphate uridylyltransferase
Function / homology: / glucose-1-phosphate thymidylyltransferase activity / Nucleotidyl transferase domain / Nucleotidyl transferase / biosynthetic process / Nucleotide-diphospho-sugar transferases / Nucleotidyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.27 Å
AuthorsShin, D.H. / Jo, S.R. / Kim, M.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1D1A1B07050781 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of PAMurU
Authors: Shin, D.H. / Jo, S.R. / Kim, M.S.
History
DepositionNov 16, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleotidyl transferase
B: Nucleotidyl transferase
C: Nucleotidyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3247
Polymers78,7983
Non-polymers5264
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.509, 76.509, 97.935
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Nucleotidyl transferase / Nucleotidyltransferase / Nucleotidyltransferase family protein


Mass: 26265.969 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: rmlA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1Y3LFE7, glucose-1-phosphate thymidylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.06M NaCl, 0.1M HEPES pH8.0, 1.6M Ammonium sulfate, 0.1M Lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 29509 / % possible obs: 100 % / Redundancy: 11.4 % / Rsym value: 0.129 / Net I/σ(I): 16.2
Reflection shellResolution: 2.27→2.31 Å / Num. unique obs: 1478 / Rsym value: 0.501

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.27→32.65 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1961 6.77 %
Rwork0.1797 --
obs0.1835 28978 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 30 269 5407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095260
X-RAY DIFFRACTIONf_angle_d1.1557145
X-RAY DIFFRACTIONf_dihedral_angle_d15.9451906
X-RAY DIFFRACTIONf_chiral_restr0.064763
X-RAY DIFFRACTIONf_plane_restr0.007950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.31191360.20661844X-RAY DIFFRACTION94
2.33-2.390.25551460.20261912X-RAY DIFFRACTION96
2.39-2.460.26231320.18321851X-RAY DIFFRACTION96
2.46-2.540.2541460.19121925X-RAY DIFFRACTION97
2.54-2.630.27051330.20441910X-RAY DIFFRACTION97
2.63-2.740.27691460.19341933X-RAY DIFFRACTION98
2.74-2.860.25191390.19461896X-RAY DIFFRACTION99
2.86-3.020.26041380.20361950X-RAY DIFFRACTION99
3.02-3.20.2621410.20251973X-RAY DIFFRACTION99
3.2-3.450.25971460.18341961X-RAY DIFFRACTION100
3.45-3.80.21291360.16161974X-RAY DIFFRACTION100
3.8-4.340.20751440.15011942X-RAY DIFFRACTION100
4.35-5.470.19771380.16021981X-RAY DIFFRACTION100
5.48-6.160.22021400.17951965X-RAY DIFFRACTION100

+
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