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- PDB-1fwy: CRYSTAL STRUCTURE OF N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSF... -

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Basic information

Entry
Database: PDB / ID: 1fwy
TitleCRYSTAL STRUCTURE OF N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE BOUND TO UDP-GLCNAC
ComponentsUDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
KeywordsTRANSFERASE / acetyltransferase / bifunctional / drug design / pyrophosphorylase
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 / identical protein binding / membrane / cytosol
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 transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...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 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
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Bifunctional protein GlmU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsBrown, K. / Pompeo, F. / Dixon, S. / Mengin-Lecreulx, D. / Cambillau, C. / Bourne, Y.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of the bifunctional N-acetylglucosamine 1-phosphate uridyltransferase from Escherichia coli: a paradigm for the related pyrophosphorylase superfamily.
Authors: Brown, K. / Pompeo, F. / Dixon, S. / Mengin-Lecreulx, D. / Cambillau, C. / Bourne, Y.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
B: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,07110
Polymers72,3482
Non-polymers1,7238
Water4,197233
1
A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,10715
Polymers108,5223
Non-polymers2,58512
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
2
B: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,10715
Polymers108,5223
Non-polymers2,58512
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
Unit cell
Length a, b, c (Å)140.780, 140.780, 244.630
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 either from chain A or B

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Components

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


Mass: 36174.090 Da / Num. of mol.: 2 / Fragment: TRUNCATED FORM AFTER R331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET-22B / Production host: Escherichia coli (E. coli)
References: UniProt: P0ACC7, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.3-1.5 M ammonium sulfate, 0.1 M MES, 4% acetone (v/v), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
22 mMacetate1drop
31.3-1.5 Mammonium sulfate1reservoir
40.1 MMES1reservoir
54 %(v/v)acetone1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 40 / % possible obs: 97.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 5.1
Reflection shell
*PLUS
% possible obs: 98.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 --random
Rwork0.217 ---
obs-40 97.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4975 0 106 233 5314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.65
X-RAY DIFFRACTIONc_torsion_deg24.7
X-RAY DIFFRACTIONc_torsion_impr_deg0.96
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 40231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

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