[English] 日本語
Yorodumi
- PDB-4m9c: WeeI from Acinetobacter baumannii AYE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m9c
TitleWeeI from Acinetobacter baumannii AYE
ComponentsBacterial transferase hexapeptide (Three repeats) family protein
KeywordsTRANSFERASE / left-handed beta-helix / rossmann fold / acetyltransferase
Function / homology
Function and homology information


acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / Rossmann fold - #20 / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid ...Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / Rossmann fold - #20 / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative acetyltransferase (WeeI) / :
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMorrison, M.J. / Imperiali, B.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Biochemical analysis and structure determination of bacterial acetyltransferases responsible for the biosynthesis of UDP-N,N'-diacetylbacillosamine.
Authors: Morrison, M.J. / Imperiali, B.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterial transferase hexapeptide (Three repeats) family protein
B: Bacterial transferase hexapeptide (Three repeats) family protein
C: Bacterial transferase hexapeptide (Three repeats) family protein
D: Bacterial transferase hexapeptide (Three repeats) family protein
E: Bacterial transferase hexapeptide (Three repeats) family protein
F: Bacterial transferase hexapeptide (Three repeats) family protein


Theoretical massNumber of molelcules
Total (without water)137,9326
Polymers137,9326
Non-polymers00
Water11,530640
1
A: Bacterial transferase hexapeptide (Three repeats) family protein
B: Bacterial transferase hexapeptide (Three repeats) family protein
C: Bacterial transferase hexapeptide (Three repeats) family protein


Theoretical massNumber of molelcules
Total (without water)68,9663
Polymers68,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-45 kcal/mol
Surface area24500 Å2
MethodPISA
2
D: Bacterial transferase hexapeptide (Three repeats) family protein
E: Bacterial transferase hexapeptide (Three repeats) family protein
F: Bacterial transferase hexapeptide (Three repeats) family protein


Theoretical massNumber of molelcules
Total (without water)68,9663
Polymers68,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-44 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.289, 148.289, 182.413
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Bacterial transferase hexapeptide (Three repeats) family protein


Mass: 22988.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AYE / Plasmid: pET30b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS RIL / References: UniProt: B7H2H9, UniProt: B0V6J7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate trihydrate, 3.0 M NaCl, 0.7% 1-butanol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2012
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→48.5 Å / Num. all: 180938 / Num. obs: 180938 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 29.25 Å2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.2 / % possible all: 97.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.54 Å
Translation2.5 Å48.54 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BSW

3bsw


Resolution: 2.1→48.5 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.29 / σ(F): 2 / Phase error: 23.02 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 6517 5 %RANDOM
Rwork0.1907 ---
obs0.1925 130237 96.42 %-
all-180938 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.532 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 106.31 Å2 / Biso mean: 34.597 Å2 / Biso min: 8.88 Å2
Baniso -1Baniso -2Baniso -3
1--7.0086 Å2-0 Å20 Å2
2---7.0086 Å2-0 Å2
3---14.0172 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9479 0 0 640 10119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079688
X-RAY DIFFRACTIONf_angle_d1.09613197
X-RAY DIFFRACTIONf_chiral_restr0.0751590
X-RAY DIFFRACTIONf_plane_restr0.0051687
X-RAY DIFFRACTIONf_dihedral_angle_d12.5683401
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.17510.25856070.2237115511215891
2.1751-2.26210.25486200.2056117131233392
2.2621-2.36510.25396480.2038119041255294
2.3651-2.48980.2596010.2167121291273095
2.4898-2.64580.27016370.2225123921302997
2.6458-2.850.27676730.2247125351320898
2.85-3.13680.25066720.2117126861335899
3.1368-3.59060.23546990.1999127181341799
3.5906-4.52320.17666730.15621291313586100
4.5232-48.55190.19956870.1682131791386699

+
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