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- PDB-1ejc: Crystal structure of unliganded mura (type2) -

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Basic information

Entry
Database: PDB / ID: 1ejc
TitleCrystal structure of unliganded mura (type2)
ComponentsUDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
KeywordsTRANSFERASE / inside-out alpha/beta barrel
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytoplasm
Similarity search - Function
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsEschenburg, S. / Schonbrunn, E.
Citation
Journal: Proteins / Year: 2000
Title: Comparative X-ray analysis of the un-liganded fosfomycin-target murA.
Authors: Eschenburg, S. / Schonbrunn, E.
#1: Journal: Biochemistry / Year: 2000
Title: Role of the Loop Containing Residue 115 in the Induced-fit Mechanism of the Bacterial Cell Wall Biosynthetic Enzyme MurA
Authors: Schonbrunn, E. / Eschenburg, S. / Krekel, F. / Luger, K. / Amrhein, N.
#2: Journal: Structure / Year: 1996
Title: Crystal Structure of UDP-N-acetylglucosamine Enolpyruvyltransferase, the Target of the Antibiotic Fosfomycin
Authors: Schonbrunn, E. / Sack, S. / Eschenburg, S. / Perrakis, A. / Krekel, F. / Amrhein, N. / Mandelkow, E.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2936
Polymers44,8291
Non-polymers4635
Water9,620534
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.385, 73.668, 77.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE / MURA / EPT


Mass: 44829.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 % PEG 20000, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130-50 mg/mlenzyme1drop
210 %PEG200001drop
30.1 MMES1drop
40.5 MMES1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 36451 / Num. obs: 36451 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.4
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.225 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 251049
Reflection shell
*PLUS
% possible obs: 99.2 % / Mean I/σ(I) obs: 5.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.8→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: HOH 1 occupies an alternate position of alternate conformation A NH1 ARG 295. HOH 1 has alternate position A.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1094 3 %RANDOM
Rwork0.167 ---
all-36451 --
obs-36451 99.6 %-
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---1.69 Å20 Å2
3---2.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 29 534 3706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d3.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 178 3 %
Rwork0.245 5742 -
obs--98.4 %
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.5

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