[English] 日本語
Yorodumi
- PDB-5vmk: Crystal structure of a bifunctional GlmU UDP-N-acetylglucosamine ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vmk
TitleCrystal structure of a bifunctional GlmU UDP-N-acetylglucosamine diphosphorylase/glucosamine-1- phosphate N-acetyltransferase from Acinetobacter baumannii
ComponentsBifunctional protein GlmU
KeywordsTRANSFERASE / NIAID / cSMRT / citrate / structural genomics / mutli-domain protein / bifunctional protein / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape / magnesium ion binding / cytoplasm
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat ...Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / Bifunctional protein GlmU / Bifunctional protein GlmU
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a bifunctional GlmU UDP-N-acetylglucosamine diphosphorylase/glucosamine-1- phosphate N-acetyltransferase from Acinetobacter baumannii
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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: Bifunctional protein GlmU
B: Bifunctional protein GlmU
C: Bifunctional protein GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,10610
Polymers149,8523
Non-polymers1,2547
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-27 kcal/mol
Surface area48050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.620, 96.620, 262.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Bifunctional protein GlmU


Mass: 49950.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: glmU, ABUW_0090 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D5YCC7, UniProt: B0VPT6*PLUS, glucosamine-1-phosphate N-acetyltransferase, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: AcbaC.00150.a.B1.PW37634 at 19.3 mg/mL against JCSG+ screen condition C6 40% PEG 300, 0.1 M phosphate-citrate pH 4.2, crystal tracking ID 261513c6, unique puck ID epp4-5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.55→47.512 Å / Num. obs: 47221 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.535 % / Biso Wilson estimate: 44.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.076 / Χ2: 0.979 / Net I/σ(I): 17.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.625.640.523.6234460.910.57499.9
2.62-2.695.6520.4534.1333270.9160.49999.9
2.69-2.775.6410.4154.3932740.9320.457100
2.77-2.855.6370.3225.6131820.9560.35599.9
2.85-2.945.6290.2227.7230640.9780.245100
2.94-3.055.6170.28.5729870.9840.221100
3.05-3.165.6130.14811.2828700.990.16399.9
3.16-3.295.6030.1114.327810.9950.12199.9
3.29-3.445.6030.08916.826780.9970.099100
3.44-3.615.5620.0720.6225510.9980.07799.9
3.61-3.85.5350.05524.724570.9990.06199.8
3.8-4.035.5460.0527.0623150.9990.05599.9
4.03-4.315.4680.04131.4621730.9990.04699.8
4.31-4.665.4270.03433.1820460.9990.03899.4
4.66-5.15.4660.03434.4918730.9990.03899.2
5.1-5.75.3860.03733.8217300.9990.04199.9
5.7-6.585.3340.03434.9515180.9990.03899.8
6.58-8.065.2550.02839.97131810.03199.8
8.06-11.44.9720.02249.02104110.02599.7
11.4-47.5124.4660.02147.0259010.02491.6

-
Processing

Software
NameVersionClassification
PHENIX(dev_2744: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2oi6

2oi6


Resolution: 2.55→47.512 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 1943 4.13 %
Rwork0.1846 --
obs0.1872 47068 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→47.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9271 0 83 308 9662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079483
X-RAY DIFFRACTIONf_angle_d0.88412892
X-RAY DIFFRACTIONf_dihedral_angle_d14.3745608
X-RAY DIFFRACTIONf_chiral_restr0.0571548
X-RAY DIFFRACTIONf_plane_restr0.0061693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.61380.30481460.21623185X-RAY DIFFRACTION100
2.6138-2.68450.27891370.21013167X-RAY DIFFRACTION100
2.6845-2.76340.27281240.21173190X-RAY DIFFRACTION100
2.7634-2.85260.28091400.21043187X-RAY DIFFRACTION100
2.8526-2.95460.32071140.19973180X-RAY DIFFRACTION100
2.9546-3.07280.28771200.20193232X-RAY DIFFRACTION100
3.0728-3.21270.25151500.20333202X-RAY DIFFRACTION100
3.2127-3.3820.25491420.19983185X-RAY DIFFRACTION100
3.382-3.59380.27231240.1843260X-RAY DIFFRACTION100
3.5938-3.87120.23831600.1643193X-RAY DIFFRACTION100
3.8712-4.26050.20581200.14813248X-RAY DIFFRACTION100
4.2605-4.87650.20491430.14423208X-RAY DIFFRACTION98
4.8765-6.14180.23661650.19293279X-RAY DIFFRACTION100
6.1418-47.51980.25161580.20343409X-RAY DIFFRACTION98
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)
13.3021-0.42891.88831.6817-0.54494.05190.1-0.0745-0.2636-0.04-0.2001-0.28370.28250.71690.08580.37380.0774-0.03070.63010.08030.352413.5693-43.5058-17.4492
21.2794-0.43880.54161.15990.0222.81190.04790.17870.2067-0.4269-0.0365-0.2137-0.15680.15520.01820.3579-0.03890.05460.27060.01460.3027-4.4317-24.1781-54.5488
31.10310.2822-1.02284.29292.15442.57590.0233-0.14081.694-0.90180.1888-0.5991-0.9771-0.0131-0.10460.78440.0336-0.0560.3811-0.16860.9743-15.08020.8967-31.4125
40.4527-0.4263-0.57721.24381.31011.7486-0.2067-1.31961.05050.20550.07320.2256-0.2767-0.26310.18330.65210.2524-0.06330.9674-0.57480.918-20.7905-2.5327-15.0825
51.1058-0.6946-0.00571.92650.72432.82740.12730.30820.0055-0.4849-0.16280.1735-0.2341-0.23120.05920.35580.0605-0.04930.3357-0.0210.301-25.6706-25.8234-58.6556
62.6720.0755-0.17782.6401-1.83852.34020.0117-0.6211-0.70680.52140.63580.9479-0.0694-0.9606-0.34830.543-0.05070.13150.83890.27710.8409-39.6614-47.124-19.4706
71.0223-0.3644-0.25721.33780.46531.77520.12250.2223-0.1861-0.2708-0.09010.04610.04790.067-0.01480.30910.015-0.04920.2381-0.04240.2976-14.1593-42.4896-54.1257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 225 )
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 450 )
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 78 )
4X-RAY DIFFRACTION4chain 'B' and (resid 79 through 247 )
5X-RAY DIFFRACTION5chain 'B' and (resid 248 through 449 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 225 )
7X-RAY DIFFRACTION7chain 'C' and (resid 226 through 450 )

+
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