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- PDB-3fww: The crystal structure of the bifunctional N-acetylglucosamine-1-p... -

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Basic information

Entry
Database: PDB / ID: 3fww
TitleThe crystal structure of the bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase from Yersinia pestis CO92
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE / N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase / structural genomics / CSGID / Acyltransferase / Cell shape / Cell wall biogenesis/degradation / Magnesium / Metal-binding / Multifunctional enzyme / Nucleotidyltransferase / Peptidoglycan synthesis / Center for Structural Genomics of Infectious Diseases
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 transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) ...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 / 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
Bifunctional protein GlmU
Similarity search - Component
Biological speciesYersinia pestis Pestoides F (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, R. / Gu, M. / Stam, J. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of the bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase from Yersinia pestis CO92
Authors: Zhang, R. / Gu, M. / Anderson, W. / Joachimiak, A.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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Assembly

Deposited unit
A: Bifunctional protein glmU


Theoretical massNumber of molelcules
Total (without water)48,9021
Polymers48,9021
Non-polymers00
Water45025
1
A: Bifunctional protein glmU
x 6


Theoretical massNumber of molelcules
Total (without water)293,4106
Polymers293,4106
Non-polymers00
Water1086
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
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area26520 Å2
ΔGint-111 kcal/mol
Surface area102060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.318, 88.318, 251.931
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Bifunctional protein glmU / / UDP-N-acetylglucosamine pyrophosphorylase / N-acetylglucosamine-1-phosphate uridyltransferase / ...UDP-N-acetylglucosamine pyrophosphorylase / N-acetylglucosamine-1-phosphate uridyltransferase / Glucosamine-1-phosphate N-acetyltransferase


Mass: 48901.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis Pestoides F (bacteria) / Strain: CO92 / Gene: gi: 16124227, glmU, YPDSF_3916 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: A4TSJ5, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17M Sodium Acetate, Tris-HCl, 25.5% PEG4000, 15% Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→34.804 Å / Num. all: 21276 / Num. obs: 20468 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 31.96
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 1.58 / % possible all: 87.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MERLOTphasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HV9

1hv9


Resolution: 2.5→34.804 Å / SU ML: 0.41 / σ(F): 1.89 / Phase error: 29.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 1050 5.13 %
Rwork0.2142 --
obs0.2173 20468 96.2 %
all-21276 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.871 Å2 / ksol: 0.314 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→34.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 25 3355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073409
X-RAY DIFFRACTIONf_angle_d1.0784627
X-RAY DIFFRACTIONf_dihedral_angle_d19.2891232
X-RAY DIFFRACTIONf_chiral_restr0.067546
X-RAY DIFFRACTIONf_plane_restr0.004607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60430.38051340.30592281X-RAY DIFFRACTION50
2.6043-2.74160.34641320.28272398X-RAY DIFFRACTION53
2.7416-2.91330.32211400.25392413X-RAY DIFFRACTION53
2.9133-3.13810.31731350.24092417X-RAY DIFFRACTION53
3.1381-3.45360.25741320.22352418X-RAY DIFFRACTION53
3.4536-3.95280.25451390.19822446X-RAY DIFFRACTION54
3.9528-4.97780.28391140.18742461X-RAY DIFFRACTION53
4.9778-34.80720.2631240.21012584X-RAY DIFFRACTION56
Refinement TLS params.Method: refined / Origin x: 35.4054 Å / Origin y: 8.1767 Å / Origin z: 20.9506 Å
111213212223313233
T0.4328 Å2-0.1357 Å2-0.0864 Å2-0.2444 Å20.0511 Å2--0.3596 Å2
L0.5454 °2-0.0539 °20.2584 °2-0.6197 °2-0.0145 °2--1.5195 °2
S0.1364 Å °-0.073 Å °-0.2146 Å °-0.0239 Å °0.0396 Å °0.0571 Å °0.6683 Å °-0.2314 Å °-0.1538 Å °
Refinement TLS groupSelection details: all

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