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- PDB-1g97: S.PNEUMONIAE GLMU COMPLEXED WITH UDP-N-ACETYLGLUCOSAMINE AND MG2+ -

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Basic information

Entry
Database: PDB / ID: 1g97
TitleS.PNEUMONIAE GLMU COMPLEXED WITH UDP-N-ACETYLGLUCOSAMINE AND MG2+
ComponentsN-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
KeywordsTRANSFERASE / GlmU / acetyltransferase / uridyltransferase / pyrophosphorylase / left-handed beta-sheet helix / trimer / magnesium / UDP-N-acetylglucosamine
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 / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / 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 / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / 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
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Bifunctional protein GlmU
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.96 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 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,0534
Polymers49,3981
Non-polymers6553
Water8,683482
1
A: N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

A: N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

A: N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,15912
Polymers148,1953
Non-polymers1,9649
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 area14460 Å2
ΔGint-97 kcal/mol
Surface area49500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.660, 93.660, 275.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-461-

NA

21A-782-

HOH

31A-814-

HOH

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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 47.9 %
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, soaked with 10 mM UDP-N-Acetylglucosamine and 10 mM Mg(Cl)2, 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 25, 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: 1.96→30 Å / Num. all: 81753 / Num. obs: 33249 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.062 / Net I/σ(I): 14.9
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 3197 / Rsym value: 0.311 / % possible all: 95.4
Reflection
*PLUS
Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 95.4 % / Rmerge(I) obs: 0.311

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Apo form of GlmU, PDB entry code 1G95

1g95


Resolution: 1.96→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 = 0.34 E/A**3, B-FACTOR = 26.9 A**2. WATER MOLECULES ARE ORDERED WITH ASCENDING B-FACTORS. THE FOLLOWING AMINO ACID RESIDUES WERE NOT VISIBLE IN ...Details: BULK SOLVENT CORRECTION WITH ELECTRON DENSITY = 0.34 E/A**3, B-FACTOR = 26.9 A**2. WATER MOLECULES ARE ORDERED WITH ASCENDING B-FACTORS. THE FOLLOWING AMINO ACID RESIDUES WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS: 1 and 448-459. THE FOLLOWING AMINO ACIDS HAVE HIGH AVERAGE B-FACTORS (>= 50 A**2) AND POOR ELECTRON DENSITY: 61, 90-92, 120-122, 145-146, 179, 188-190, 387-391, 441, 447.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1658 4.9 %RANDOM
Rwork0.188 ---
all-33249 --
obs-33242 98 %-
Solvent computationSolvent model: bulk solvent mask / Bsol: 26.9 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.699 Å2-6.737 Å20 Å2
2---2.699 Å20 Å2
3---5.399 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 41 482 3883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.42
X-RAY DIFFRACTIONc_mcangle_it2.13
X-RAY DIFFRACTIONc_scbond_it3.54.5
X-RAY DIFFRACTIONc_scangle_it56
LS refinement shellResolution: 1.96→2.03 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.286 155 4.6 %
Rwork0.256 3042 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ROCHE.PARAMROCHE.TOP
X-RAY DIFFRACTION3UNG.PRXUNG.TPX
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
X-RAY DIFFRACTIONc_mcbond_it1.42
X-RAY DIFFRACTIONc_scbond_it3.54.5
X-RAY DIFFRACTIONc_mcangle_it2.13
X-RAY DIFFRACTIONc_scangle_it56
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.256

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