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- PDB-5vmk: Crystal structure of a bifunctional GlmU UDP-N-acetylglucosamine ... -

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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 / lipopolysaccharide biosynthetic process / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / lipopolysaccharide biosynthetic process / 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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Citric acid


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


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


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


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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 )

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