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- PDB-1g95: CRYSTAL STRUCTURE OF S.PNEUMONIAE GLMU, APO FORM -

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Basic information

Entry
Database: PDB / ID: 1g95
TitleCRYSTAL STRUCTURE OF S.PNEUMONIAE GLMU, APO FORM
ComponentsN-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
KeywordsTRANSFERASE / GlmU / Acetyltransferase / uridyltransferase pyrophosphorylase / left-handed beta-sheet helix / trimer
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 morphogenesis / cell wall organization / 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 morphogenesis / cell wall organization / regulation of cell shape / magnesium ion binding / membrane / cytoplasm
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / Hexapeptide repeat ...Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / 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
Bifunctional protein GlmU
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.33 Å
AuthorsKostrewa, D. / D'Arcy, A. / Kamber, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structures of Streptococcus pneumoniae N-acetylglucosamine-1-phosphate uridyltransferase, GlmU, in apo form at 2.33 A resolution and in complex with UDP-N-acetylglucosamine and Mg(2+) at 1.96 A resolution.
Authors: Kostrewa, D. / D'Arcy, A. / Takacs, B. / Kamber, M.
History
DepositionNov 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)49,3981
Polymers49,3981
Non-polymers00
Water4,972276
1
A: N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE

A: N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE

A: N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)148,1953
Polymers148,1953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11130 Å2
ΔGint-52 kcal/mol
Surface area52210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.910, 94.910, 279.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -Y+1, X-Y, Z and -X+Y+1, -X+1, Z

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Components

#1: Protein N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE / GLMU / UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE


Mass: 49398.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q97R46, UDP-N-acetylglucosamine diphosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M BIS/TRIS, 0.2 M ammonium sulfate, 25 % PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
20.1 MBis-Tris1reservoir
30.2 Mammonium sulfate1reservoir
425 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 / Wavelength: 0.873 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 1998 / Details: Mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.33→30 Å / Num. all: 37195 / Num. obs: 20586 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.061 / Net I/σ(I): 10.5
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2007 / Rsym value: 0.188 / % possible all: 95.7
Reflection
*PLUS
Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 95.7 % / Rmerge(I) obs: 0.188

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.33→30 Å / Isotropic thermal model: isotropic / Cross valid method: FREE-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT CORRECTION WITH ELECTRON DENSITY = 0.26 E/A**3, B-FACTOR = 23.5 A**2. THE FOLLOWING AMINO ACID RESIDUES WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS: 188-193, 453-459. THE ...Details: BULK SOLVENT CORRECTION WITH ELECTRON DENSITY = 0.26 E/A**3, B-FACTOR = 23.5 A**2. THE FOLLOWING AMINO ACID RESIDUES WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS: 188-193, 453-459. THE ELECTRON DENSITY MAPS OF THE FOLLOWING AMINO ACID RESIDUES WERE OF RELATIVELY POOR QUALITY: 2, 10-12, 51-94, 145-149, 154-164, 179-187, 194-197, 439-441, 447-452. THE WATER MOLECULES ARE ORDERED WITH ASCENDING B-FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1039 5 %RANDOM
Rwork0.228 ---
all-20586 --
obs-20576 97 %-
Solvent computationSolvent model: bulk solvent mask / Bsol: 23.5 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.364 Å2-1.048 Å20 Å2
2---8.364 Å20 Å2
3---16.728 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.33→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 276 3634
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it2.52
X-RAY DIFFRACTIONc_mcangle_it3.83
X-RAY DIFFRACTIONc_scbond_it5.84.5
X-RAY DIFFRACTIONc_scangle_it7.36
LS refinement shellResolution: 2.33→2.41 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.35 118 5 %
Rwork0.306 1889 -
obs-1889 96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ROCHE.PARAMROCHE.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.1 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.35 / % reflection Rfree: 5 % / Rfactor Rwork: 0.306

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